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A

A_ALL - Static variable in class chemaxon.struc.graphics.MTextAttributes
All identifiers.
A_ALL - Static variable in interface chemaxon.struc.Smolecule
Use all atom and bond property arrays.
A_ASTEREO - Static variable in interface chemaxon.struc.Smolecule
Use atom stereo properties arrays, equals Smolecule.A_PARITY|Smolecule.A_CHIRALITY.
A_ATOMMAP - Static variable in interface chemaxon.struc.Smolecule
Use atom type array.
A_BOLD - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font's bold subattribute.
A_BOND - Static variable in interface chemaxon.struc.Smolecule
Use arrays to store bonds.
A_CHARGE - Static variable in interface chemaxon.struc.Smolecule
Use charge array.
A_CHIRALITY - Static variable in interface chemaxon.struc.Smolecule
Chirality.
A_DX - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the x shift attribute.
A_DY - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the y shift attribute.
A_EXPLH - Static variable in interface chemaxon.struc.Smolecule
Use explicit Hydrogen count array.
A_FONT - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font attribute.
A_FONT_BITS - Static variable in class chemaxon.struc.graphics.MTextAttributes
All font bits.
A_FONTFAMILY - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font family subattribute.
A_FONTSIZE - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font size subattribute.
A_FOREGROUND - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the color attribute.
A_HYBRIDIZATION - Static variable in interface chemaxon.struc.Smolecule
Use hybridization state array.
A_IMPLH - Static variable in interface chemaxon.struc.Smolecule
Use implicit Hydrogen count array.
A_ITALIC - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font's italic subattribute.
A_MASSNO - Static variable in interface chemaxon.struc.Smolecule
Use mass number array.
A_PARITY - Static variable in interface chemaxon.struc.Smolecule
Atom parity.
A_RADICAL - Static variable in interface chemaxon.struc.Smolecule
Use radical array.
A_RGROUP - Static variable in interface chemaxon.struc.Smolecule
Use R-group ID array.
A_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the font scale attribute.
A_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes
Identifier of the subscript/superscript level attribute.
A_VALENCE - Static variable in interface chemaxon.struc.Smolecule
Use valence array.
AAMAP_MASK - Static variable in class chemaxon.struc.MolAtom
Atom map mask in flags.
AAMAP_MAX - Static variable in class chemaxon.struc.MolAtom
Maximum atom-atom mapping number.
AAMAP_OFF - Static variable in class chemaxon.struc.MolAtom
Atom map offset in flags.
AATOM - Static variable in class chemaxon.jep.context.ReactionContext
 
ABBREVGROUP - Static variable in class chemaxon.formats.MFileFormat
ChemAxon SMILES Abbreviated Groups.
AbbrevGroupRecognizer - Class in chemaxon.formats.recognizer
Deprecated.
as of Marvin 2014.07.21.0 intended for internal use only
AbbrevGroupRecognizer() - Constructor for class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated.
 
ABBREVIATED_GROUPS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "abbrevgroups".
ABBREVIATED_GROUPS_ALLOWED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "abbrevgroupsAllowed".
AbbreviatedGroupChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
AbbreviatedGroupChecker() - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker
Default constructor.
AbbreviatedGroupChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker
Parameterized constructor.
ABS_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Absolute stereoconfiguration label visibility flag.
ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants
Option for absolute stereo matching.
ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants
Option for absolute stereo matching.
ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants
Option for absolute stereo matching.
AbsentChiralFlagChecker - Class in chemaxon.checkers
Detects chiral molecules with no chiral flag defined
AbsentChiralFlagChecker() - Constructor for class chemaxon.checkers.AbsentChiralFlagChecker
Initializes the absent chiral flag error checker
AbsentChiralFlagFixer - Class in chemaxon.fixers
Deprecated.
AbsentChiralFlagFixer() - Constructor for class chemaxon.fixers.AbsentChiralFlagFixer
Deprecated.
 
ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show absolute stereo label.
ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "absLabelVisible" or "absLabel".
AbsoluteStereoConfigurationChecker - Class in chemaxon.checkers
Detects molecules in which all asymmetric centers have absolute stereo configuration
AbsoluteStereoConfigurationChecker() - Constructor for class chemaxon.checkers.AbsoluteStereoConfigurationChecker
Initializes the absolute stereo configuration checker
AbsoluteStereoFixer - Class in chemaxon.fixers
AbsoluteStereoFixer() - Constructor for class chemaxon.fixers.AbsoluteStereoFixer
Deprecated.
 
AbstractMRecordReader - Class in chemaxon.marvin.io.formats
Abstract record reader class.
AbstractMRecordReader(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader
Constructs an abstract record reader.
AbstractMRecordReader(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader
 
AbstractStereoFilter<T extends StereoCenter> - Class in com.chemaxon.calculations.stereoanal.filters
Abstract class for Filter interface.
AbstractStereoFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
 
AbstractStructureChecker - Class in chemaxon.checkers
Abstract base class of all functions checking and repairing chemical structures.
AbstractStructureChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AbstractStructureChecker
Constructor to create a Structure checker instance with the given errorType
AbstractStructureFixer - Class in chemaxon.fixers
This class is the default abstract implementation of StructureFixer interface
AbstractStructureFixer() - Constructor for class chemaxon.fixers.AbstractStructureFixer
Constructor to create a Structure fixer
Ac - Static variable in class chemaxon.core.ChemConst
 
accept(Molecule) - Method in class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter
Accepts molecule if the number of R-group attachments in the molecule is exactly the attachment count specified in the constructor of this filter.
accept(Molecule) - Method in interface chemaxon.util.MolFilter
Returns true if molecule is accepted by the filter.
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
 
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
 
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
 
accept(StereoCenterVisitor) - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
Accepts visitors.
accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
 
acceptElements(boolean) - Method in class chemaxon.naming.DocumentExtractor
Deprecated.
 
acceptGenericNames(boolean) - Method in class chemaxon.naming.DocumentExtractor
Deprecated.
Whether to accept generic, frequent names like "water".
acceptGroups(boolean) - Method in class chemaxon.naming.DocumentExtractor
Deprecated.
 
acceptIons(boolean) - Method in class chemaxon.naming.DocumentExtractor
Deprecated.
 
ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
Acceptor sign displayed in GUI.
ACCEPTOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
ACCORD - Static variable in class chemaxon.formats.MFileFormat
ACCORD file format
ACCP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Constant denoting acidic pKa.
actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
Action handler.
ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
action string token of the checker
ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor
action string tokens of the fixer
ActionStringBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader
An implementation of ConfigurationReader for parsing action strings
ActionStringBasedConfigurationReader(String) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
Default constructor
ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
ActionStringBasedConfigurationReader(String, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
Constructor with custom checker factory
activateContainerCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
The containing cell of the GraphicComponent will be the active cell of the scene.
active - Variable in class chemaxon.marvin.space.GraphicComponent
Is this component selected or not.
add(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
Add a name to structure converter.
add(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Calculates the sum of the two vectors
add(DPoint3) - Method in class chemaxon.struc.DPoint3
Add the given point to this one.
add(MolBond) - Method in class chemaxon.struc.MolAtom
Add a bond if it had not been already added.
add(MolBond) - Method in class chemaxon.struc.Molecule
Adds a bond to the molecule.
add(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom to the molecule.
add(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond to the molecule.
add(MolBond, boolean) - Method in class chemaxon.struc.MoleculeGraph
Add a bond to the molecule.
add(MProp) - Method in class chemaxon.struc.prop.MListProp
Adds an element.
add(MolAtom) - Method in class chemaxon.struc.RgMolecule
Adds an atom to the root structure.
add(MolBond) - Method in class chemaxon.struc.RgMolecule
Adds a bond to the root structure.
add(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Adds an atom to a reactant, product or agent 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, boolean) - Method in class chemaxon.struc.SelectionMolecule
Add a bond to the molecule.
add(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom to the molecule.
add(MolAtom, boolean) - 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(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
Add an edge if it had not been already added.
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(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new atom to the S-group.
ADD_REMOVE_H_ATOMS_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "addRemoveHatomsEnabled".
addActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane
Adds an action listener.
addActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions
Adds an action listener.
addAtom(Smolecule, int) - Method in interface chemaxon.struc.WSmolecule
Adds an atom from another Smolecule.
addAtom(int) - Method in interface chemaxon.struc.WSmolecule
Adds an atom.
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, double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Adds an alignment constraint between the reference and aligned molecule.
addAtomPair(int, int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Adds an alignment constraint between the reference and aligned molecule.
addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Adds all atoms and bonds to the specified molecule.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.Molecule
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RgMolecule
Adds an atom to a fragment.
addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Adds an atom to a fragment.
addAtomWithBonds(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom to the molecule.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds an atom without setting its parentGraph and index fields.
addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
Adds an atom without setting its parentGraph and index fields.
addAttachmentPoint(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point for an atom.
addAttachmentPoint(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point of the given attachment atom and order.
addAttachmentPoint(MolAtom, int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Adds a new free attachment point.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MBracket
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MEFlow
 
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MPolyline
Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRectangle
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRoundedRectangle
Adds the attribute names to the specified vector.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
Adds the attribute names to the specified list.
addAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
Adds the attribute names to the specified list.
addBond(int, int, int) - Method in interface chemaxon.struc.WSmolecule
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.Molecule
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond.
addBond0(MolBond) - Method in class chemaxon.struc.SelectionMolecule
Adds a bond.
addBondWithoutChangingIt(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Adds a bond without setting its parentGraph and index fields.
addBracket(MBracket) - Method in class chemaxon.struc.Sgroup
Adds a bracket to this S-group.
addCanvas(Container) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace viewer to the container.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
Adds attribute names to the specified list.
addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
Adds attribute names to the specified list.
addCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Adds a central atom to this sgroup.
addChar(char) - Method in class chemaxon.struc.graphics.MTextBox
Adds a character to the text.
addCheckerMark(MDocument.CheckerMark) - Method in class chemaxon.struc.MDocument
Adds a checker mark to the document.
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
 
addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Adds a new component to this cell.
addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to the active or to the first cell.
addComponent(GraphicComponent, int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to the cell having the given index.
addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule
Adds a reactant, product or agent.
addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule
Adds a reactant, product or agent.
addComponentToEmptyCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Adds a component to an empty cell.
addConstraintsFromUserMappedAtoms() - Method in class chemaxon.marvin.alignment.Alignment
An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.
addCoordinateSystem(int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a dummy graphic component that represents the coordinate system.
addCrossingBonds(List<MolBond>, List<MolBond>) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Sets the crossing bonds (head and tail) of a ladder-type polymer.
addData(Molecule, MolAtom, String, String) - Method in class chemaxon.marvin.io.MolExportModule
Adds a data sgroup to the given atom in the given molecule with fieldName and value.
addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup
Adds a line to the data stored in the field.
addDihedralStep(DihedralScanStep) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
Add a new step.
addDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent
Forces the component to set all drawing property stored in drawProperties, and leaves the old settings which are not overidden.
addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:
Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
addExplicitHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:
Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
addExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]).
Usage:
Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
addFunction(String, PostfixMathCommandI) - Method in class chemaxon.jep.ChemJEP
Adds a new function to the parser.
addHAtoms(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead
addHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph) instead
addHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) instead
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.
addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Builder
Adds an input stream.
addInput(File, String) - Method in class chemaxon.formats.MolConverter.Builder
Adds an input file.
addInput(String, String) - Method in class chemaxon.formats.MolConverter.Builder
Adds an input file.
addInput(File, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
addInput(String, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a label component inside the MarvinView table.
addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
Defines a label component inside the MarvinView table.
addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MTextBox
 
addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage
Adds a listener if it is not yet added.
addListToDelete(int) - Method in class chemaxon.marvin.space.GraphicScene
Adds a gl list id to the deletion list
addLonePairs(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Deprecated.
since Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead
addMatch(int[], int[], int) - Method in class chemaxon.sss.search.Search
Specifies extra prerequisites of the structure search that queryAtoms[0] must match to targetAtoms[0] only AND queryAtoms[1] must match to targetAtoms[1], etc.
addMatch(int, int) - Method in interface com.chemaxon.search.SimpleSearcher
Adds a fixed matching between the given query and target atoms.
addMenuBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace menubar to the container.
addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane
Adds a menubar change listener.
addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment
Add molecule to align
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(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.
addMolecule(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds a Molecule object to the actual cell of the viewer.
addMoleculeTo(Molecule, int) - Method in class chemaxon.marvin.space.MSpaceEasy
Makes the given cell to be the active cell, and adds the molecule to it.
addMoleculeToEmptyCell(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.
addMoleculeToEmptyCell(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.
addMoleculeWithoutChange(Molecule, boolean) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds a Molecule object to the actual cell of the viewer and resets the view only if required.
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.Alignment
User may define extra weights between colors defined at setColoringScheme.
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
 
addNodeColorWeight(int, int, double) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
 
addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
 
addNotify() - Method in class chemaxon.struc.graphics.MMidPoint
Point added to a document.
addNotify() - Method in class chemaxon.struc.graphics.MRectanglePoint
Point added to a document.
addNotify() - Method in class chemaxon.struc.MObject
Deprecated.
As of Marvin 6.1, replaced by MObject.addNotify(MDocument). Will be removed after October 1 2017.
addNotify(MDocument) - Method in class chemaxon.struc.MObject
Called when the object is added to a document.
addNumbering - Variable in class chemaxon.marvin.io.MolExportModule
Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.
addObject(MObject) - Method in class chemaxon.struc.MDocument
Adds an object to the document.
addObject(MObject) - Method in class chemaxon.struc.MSelectionDocument
Adds an object to the document.
addOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Adds an owner, that should be notified about the changes in the properties.
addPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
addPopupMenu() - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace popup menu to the JPanel.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
 
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner
Adds a PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner
Adds a PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with the given name is changed
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
Add a PropertyChangeListener for a specific property.
addPropertyChangeListener(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(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
Add a PropertyChangeListener for a specific property.
addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
Add a PropertyChangeListener to the listener list.
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(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
Add a property change listener
addReactionStep(List<Molecule>, List<Molecule>, List<Molecule>, MRArrow, int) - Method in class chemaxon.struc.RxnMolecule
 
addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Adds an atom to the list of paradigmatic repeating unit atoms.
addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule
Adds an R-group member.
addRgroupAttachmentPoint(int, int) - Method in class chemaxon.struc.MolAtom
Attaches a new R-group attachment point to this atom by a bond of a specified type.
addRgroupBridgeMember(RgroupBridgeId, Molecule) - Method in class chemaxon.struc.RgMolecule
Adds a definition member to an R-group bridge.
addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule
Creates an RgMolecule containing R-groups of this object from the 'simplified molecule' object made of 'm'.
addSelectionPanel(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
addSelectionPanelAndProgressBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.Molecule
Adds an S-group to this object.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule
Adds an S-group to this object.
addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule
Adds an S-group to this object.
addSgroupClones(Molecule, Molecule, Molecule) - Method in class chemaxon.struc.Molecule
Adds the S-groups of a child molecule clone to the new parent molecule clone.
addSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule
Adds S-groups to this object and its parent.
addSimpleAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Adds a non-SgroupAtom atom without setting its parentGraph and index fields.
addStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Changes terminal carbon atoms to star atoms (*).
addString(String) - Method in class chemaxon.struc.graphics.MTextBox
Adds a string to the text.
addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
Add a thread-local name to structure converter.
addToolBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace toolbar to the container.
addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
Deprecated.
Not used.
addToSelection(MDocument, MSelectionDocument) - Static method in class chemaxon.struc.NoStructure
Adds the selected NoStrutures from the document to the selectionDocument
addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
Add an element to marvinsketch's recent file list
addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
Add an element to marvinview's recent file list
addTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Add a TransferableDescriptor to the MTransferable Registry.
addTransferable(String, String, Integer, Integer, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Add a TransferableDescriptor to the registry, and constructing it by the given parameters.
addUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
Adds the given user-defined comparator to the search.
addUserConstraint(int, int, int, int) - Method in class chemaxon.marvin.alignment.Alignment
Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph
Checks whether the molecule has multiple chiral centres
AdvancedCheckerRunner - Class in chemaxon.checkers.runner
CheckerRunner implementation with advanced fixing capabilities.
StructureFixer selection is based on provided fixer class if available, or falls back to StructureCheckerResult based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts.
AdvancedCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
AdvancedCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
Constructs CheckerRunner with more advanced fixing capabilities.
Ag - Static variable in class chemaxon.core.ChemConst
 
AGENT - Static variable in class chemaxon.jep.context.ReactionContext
 
AGENTS - Static variable in class chemaxon.struc.RxnMolecule
"Agent" structure type.
Al - Static variable in class chemaxon.core.ChemConst
 
alias - Variable in class chemaxon.marvin.services.ServiceArgument
the alias of the argument
AliasChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting atoms with alias labels.
AliasChecker() - Constructor for class chemaxon.checkers.AliasChecker
Default constructor.
align() - Method in class chemaxon.marvin.alignment.Alignment
3D alignment on two or more molecules.
align() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
align() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
does a simple one-to-one atom mappin and aligns.
align(int[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
Rigid alignment on the user defined atom index
align(Molecule) - Method in interface chemaxon.marvin.alignment.MCSAlignment
Align the given molecule to the reference.
align() - Method in class chemaxon.util.MolAligner
Execute best alignment based on hit map provided earlier
align(int[]) - Method in class chemaxon.util.MolAligner
Calculates and performs the best alignment possible specified by the hit map array.
ALIGN_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 - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Alignment
Alignment - Class in chemaxon.marvin.alignment
3D Alignment aligns two or more 3D molecules onto each other.
Alignment() - Constructor for class chemaxon.marvin.alignment.Alignment
 
Alignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.Alignment
 
AlignmentAccuracyMode - Enum in chemaxon.marvin.alignment
Settings for the representation of a molecular shape.
AlignmentMolecule - Class in chemaxon.marvin.alignment
 
AlignmentMoleculeFactory - Class in chemaxon.marvin.alignment
Creates an AlignmentMolecule form a Molecule based on the settings.
AlignmentMoleculeFactory() - Constructor for class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.marvin.alignment
 
AlignmentPlugin - Class in chemaxon.marvin.calculations
Plugin layer for the AlignmentAPI
AlignmentPlugin() - Constructor for class chemaxon.marvin.calculations.AlignmentPlugin
 
AlignmentProperties - Enum in chemaxon.marvin.alignment
 
AlignmentProperties.ColoringScheme - Enum in chemaxon.marvin.alignment
 
AlignmentProperties.ColorNotSpecifiedCase - Enum in chemaxon.marvin.alignment
 
AlignmentProperties.DegreeOfFreedomType - Enum in chemaxon.marvin.alignment
 
AlignmentProperties.FlexibilityMode - Enum in chemaxon.marvin.alignment
Conformational flexibility treatment during the alignment for a pair of a molecule.
AlignmentProperties.NodeType - Enum in chemaxon.marvin.alignment
 
AlignmentProperties.OrientationType - Enum in chemaxon.marvin.alignment
 
AlignOnPairedAtoms - Class in chemaxon.marvin.alignment
Overlays two molecules using the user defined atom pairs
Example:
AlignOnPairedAtoms() - Constructor for class chemaxon.marvin.alignment.AlignOnPairedAtoms
 
AlignRigidEasy - Class in chemaxon.marvin.alignment
Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.
AlignRigidEasy() - Constructor for class chemaxon.marvin.alignment.AlignRigidEasy
 
ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
Aliphatic query atom.
ALIPHATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
aliphaticAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.
aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aliphaticAtomCount()
aliphaticBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.
aliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aliphaticBondCount()
aliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of aliphatic ring systems of the molecule.
aliphaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
aliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aliphaticRingCount()
aliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aliphaticRingCount(int)
aliphaticRings() - Method in class chemaxon.calculations.Ring
Identifies the aliphatic rings in the molecule.
aliphaticRings(int) - Method in class chemaxon.calculations.Ring
Identifies aliphatic rings in the molecule having a given size (number of atoms).
aliphaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aliphaticRings()
aliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aliphaticRings(int)
ALL_H - Static variable in class chemaxon.struc.MolAtom
Include any Hydrogen atom.
allStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
All stereo centers of molecule.
allStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
All stereo centers with attached data.
Am - Static variable in class chemaxon.core.ChemConst
 
ambient - Static variable in class chemaxon.marvin.space.monitor.Control
 
AMINOACID_BOND_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "aminoAcidBondColoringEnabled".
ANCHOR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AND_OR - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Set of enhanced stereo flags.
angle2D(double, double) - Method in class chemaxon.struc.DPoint3
Calculates the absolute angle in the XY plane of the vector pointing from this point to the other point.
angle3D(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculate the angle of two vectors (this and p) in the range 0.0 through pi.
ANGLE_STEP - Static variable in class chemaxon.struc.MolAtom
 
AngleMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring angle between 3 components, the first 2 determines a line, the second 2 another.
AngleMonitor() - Constructor for class chemaxon.marvin.space.monitor.AngleMonitor
Creates a new instance of AngleMonitor
ANIMATE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animate".
ANIMATION_DELAY - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animDelay".
ANIMATION_FPS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animFPS".
ANIMATION_SYNCHRONIZATION - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "animSync".
ANIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
ANTI - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, anti (relative configuration).
ANY - Static variable in class chemaxon.struc.MolAtom
"Atomic number" of the any atom A.
ANY - Static variable in class chemaxon.struc.MolBond
Any bond type.
ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
 
ANYBOND_AUTO - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_AUTO_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_DASHED - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_DASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_SOLID - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
ANYBOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
Use AnyBondStyle instead.
anyBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the drawing style for ANY bonds.
AnyBondStyle - Enum in chemaxon.marvin.paint.constants
Holds the values for the possible rendering styles for Any bonds.
anyCancelled(CancelObserver...) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a cancel observer which cancels when any of the specified observer is cancelled.
append(String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
Append text to end of document.
appendChars(int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append a character n times to the string buffer.
appendLeft(String, int) - Method in class chemaxon.marvin.io.MolExportModule
Append a string to the buffer in %-ns format.
appendLine(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Appends line to string buffer with closing '\n' character.
appendLines(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Appends lines to string buffer with closing '\n' character if it is not yet present.
appendMEnd(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Appends the "M END" line to the string buffer.
appendpHText(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Appends the pH text.
appendRight(String, int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append a string to the buffer in the right hand side of an n-characters wide field.
appendRight(int, int, char) - Method in class chemaxon.marvin.io.MolExportModule
Append an integer to the buffer in the right hand side of an n-characters wide field.
APPLY_DEPTH_CUE - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
As of Marvin 5.4.1, replaced by DispOptConsts.AUTOMATIC_FOG
applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane
Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.
applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane
Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.
Ar - Static variable in class chemaxon.core.ChemConst
 
ARC_BRACES - Static variable in class chemaxon.struc.graphics.MBracket
The default arc angle of the Braces Rectangle in degrees.
ARC_ROUND - Static variable in class chemaxon.struc.graphics.MBracket
The default arc angle of the Rounded Rectangle in degrees.
areAttachmentPointsVisible() - Method in class chemaxon.marvin.MolPrinter
Gets the attachment points visibility.
areChildSgroupsVisible() - Method in class chemaxon.struc.Sgroup
Checks whether the child S-groups are visible.
areChildSgroupsVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the child S-groups are visible.
areMonomersTransformed() - Method in class chemaxon.sss.search.SearchOptions
Obtain monomer transformation information.
areNeighbors(int, int) - Method in interface chemaxon.struc.Smolecule
Tests whether two atoms are connected.
arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
Are popup menus enabled?
areRGroupsHidden() - Method in class chemaxon.marvin.io.image.ImageExporter
 
AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph
Aromatization type for ambiguous 5-membered rings.
AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph
Basic aromatization.
AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph
Huckel aromatization.
AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
General (Daylight conform) aromatization.
AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph
Loose aromatization.
AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph
Substructure aromatization.
AROMATIC - Static variable in class chemaxon.struc.MolAtom
Aromatic query atom.
AROMATIC - Static variable in class chemaxon.struc.MolBond
Aromatic bond type.
AROMATIC_ATOM - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
Aromatic or aliphatic query atom.
AROMATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
AROMATIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
aromaticAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic atoms in the molecule.
aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aromaticAtomCount()
aromaticBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic bonds in the molecule.
aromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aromaticBondCount()
AromaticityCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying aromaticity problems, thus errorType property is StructureCheckerErrorType.AROMATICITY
AromaticityCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AromaticityCheckerResult
Constructor which initialize all the properties.
AromaticityErrorChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting aromatization problems.
AromaticityErrorChecker() - Constructor for class chemaxon.checkers.AromaticityErrorChecker
Default constructor.
AromaticityErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AromaticityErrorChecker
Parameterized constructor.
aromaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of all aromatic ring systems in the molecule (SSSR).
aromaticRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
aromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aromaticRingCount()
aromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aromaticRingCount(int)
aromaticRings() - Method in class chemaxon.calculations.Ring
Identifies the aromatic rings in the molecule.
aromaticRings(int) - Method in class chemaxon.calculations.Ring
Indentifies aromatic rings in the molecule having a given size (number of rings).
aromaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aromaticRings()
aromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.aromaticRings(int)
aromatize - Variable in class chemaxon.marvin.io.MolExportModule
Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, etc, dearomatize if -1, do nothing if 0.
aromatize(int, String, boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Aromatize or dearomatize molecule in the specified cell.
aromatize(int) - Method in class chemaxon.struc.Molecule
Aromatizes molecule.
aromatize(int, boolean) - Method in class chemaxon.struc.Molecule
Aromatizes molecule.
aromatize(boolean) - Method in class chemaxon.struc.MoleculeGraph
Aromatize (using the default general aromatization method) or dearomatize molecule.
aromatize() - Method in class chemaxon.struc.MoleculeGraph
Aromatize molecule using the default general aromatization method.
aromatize(int) - Method in class chemaxon.struc.MoleculeGraph
Aromatizes molecule.
aromatize(int, boolean) - 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.RgMolecule
Aromatizes molecule.
aromatizeAll(boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Aromatize or dearomatize molecules in all cells.
Aromatizer - Enum in com.chemaxon.search.transformation.transformers
Aromatizer transformer.
arrangeComponents(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges molecule components (reactants, agents, products, R-group definitions) nicely.
arrangeComponents(MoleculeGraph, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
arrangeComponents(MoleculeGraph, boolean, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
arrangeComponents() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 5.7, replaced by CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean).
Usage:
CleanUtil.arrangeComponents(molecule, true, true);
arrangeCrossingBonds(MolBond, Molecule, boolean) - Static method in class chemaxon.marvin.util.MoleculeUtil
Deprecated.
as of Marvin 5.11.1 use MoleculeGraph.setBond(int, MolBond)
arrangeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange data attached to DataSgroup.
arrangeHydrogenIncerments(Molecule, int, String, double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
arrangeMolecules(MoleculeGraph[], int, int) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice.
arrangeReaction(RxnMolecule) - Static method in class chemaxon.marvin.util.CleanUtil
Arranges reaction components nicely
arrangeRelativeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange data attached to DataSgroup.
arrangeRgroupMembers(RgMolecule) - Method in class chemaxon.marvin.util.MolFragLoader
Arranges R-group definition member coordinates.
arrangeSgBrackets(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Arrange sgroup brackets in the molecule.
ArrayMDocSource - Class in chemaxon.marvin.io
MDocSource implementation for an array of documents or molecules.
ArrayMDocSource(List<?>) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for a list of documents or molecules.
ArrayMDocSource(MDocument[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for an array of documents.
ArrayMDocSource(Molecule[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
Creates a document source for an array of molecules.
ARROW_BACK_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Arrow points back.
ARROW_CROSSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Crossed arrow flag.
ARROW_CURVED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Curved arrow flag.
ARROW_DASHED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Dashed arrow flag.
ARROW_EQUILIBRIUM_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Equilibrium arrow flag.
ARROW_GROUP1_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
Mask for the equilibrium and retrosynthetic arrow flags.
ARROW_GROUP2_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
Mask for the curved, dashed and crosed arrow flags.
ARROW_HALF_LEFT - Static variable in class chemaxon.struc.graphics.MPolyline
Only the left half of the arrow head is drawn.
ARROW_HALF_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
Unshifted mask of the half arrow option bits in flags.
ARROW_HALF_RIGHT - Static variable in class chemaxon.struc.graphics.MPolyline
Only the right half of the arrow head is drawn.
ARROW_RETROSYNTHETIC_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Retrosynthetic arrow flag.
arrowFlags - Variable in class chemaxon.struc.graphics.MPolyline
Arrow flags.
As - Static variable in class chemaxon.core.ChemConst
 
asProperties(String) - Method in class chemaxon.marvin.common.UserSettings
 
associate(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
The given component will depend on this component.
associatedComponents - Variable in class chemaxon.marvin.space.GraphicComponent
Strores components that depend on this component.
asymmetricAtomCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of atoms having four different ligands.
asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Stereochemistry.asymmetricAtomCount()
asymmetricAtoms() - Method in class chemaxon.calculations.stereo.Stereochemistry
Retrieves the indexes of atom having four different ligands.
asymmetricAtoms() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Stereochemistry.asymmetricAtoms()
AsyncCallback<T> - Interface in chemaxon.marvin.services
Callback interface for asynchronous service calls
At - Static variable in class chemaxon.core.ChemConst
 
ATMAP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom mapping flag.
ATNUM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom numbers flag.
ATOM - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Calculation domain type: calculation refers to atoms.
atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
The atom whose the neighbours are processed.
ATOM_ATOM_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
This String represents the key of cloned atom, original atom map
ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomFont".
ATOM_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Sets the atom font.
ATOM_FONT_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomFontSize".
ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomMappingVisible".
ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Displays atom mapping.
ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomNumberingType".
ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Atom numbering type
ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
in 6.2.0 use atomNumberingType parameter instead.
ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Displays atom numbers.
ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomPropertiesVisible".
ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
 
ATOM_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by mapping atom based property values to the surface.
ATOM_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "atomSet".
ATOM_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomSetColor".
ATOM_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomsize".
ATOM_STRINGS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "atomStrings".
ATOM_SYMBOL_VISIBLE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
 
ATOM_SYMBOLS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "atomSymbolsVisible".
ATOM_TYPE_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.
atomA - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
atomAndBondColors(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Set the atom and bond colors.
atomB - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
AtomChecker - Class in chemaxon.checkers
Descendants of the abstract AtomChecker class check every atom for a specific error or property.
AtomChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomChecker
Constructor to create a Structure checker instance with the given errorType.
AtomContext - Class in chemaxon.jep.context
Expression evaluation context containing an input molecule and an input atom.
AtomContext() - Constructor for class chemaxon.jep.context.AtomContext
Constructor.
atomCount() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms in the molecule.
atomCount(int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the number of atoms of a given element in the molecule.
atomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of atoms in the molecule including implicit hydrogens.
atomCount - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
atomCount - Variable in class chemaxon.struc.MoleculeGraph
The number of atoms.
atomCount() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms in the molecule.
atomCount(int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms of a given element in the molecule (including its isotopes).
atomCount(int, int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the number of atoms of a given element in the molecule.
atomFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Atom font type.
AtomIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomIterator
Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
atomLabelSize(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the atom label font size.
ATOMLIST - Static variable in class chemaxon.sss.search.MarkushFeature
Expansion type: atom list.
AtomMapChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atom maps.
AtomMapChecker() - Constructor for class chemaxon.checkers.AtomMapChecker
Default constructor
atomMapMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
atomMapMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether atom map numbers should be considered in search.
atomMapMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
atomMapping() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
Array of atom - atom mapping.
atomMapping() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Displays atom mapping.
AtomNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
Constructs an iterator to process the atoms connecting to the specified atom according to the atom and bond related behavior of this factory.
atomNumber() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Displays atom numbers.
atomNumberType(ImageExporter.AtomNumberingType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the type of atom numbering: Atom numbers or IUPAC numbering.
AtomProperty - Class in chemaxon.marvin.space
The AtomProperty class provides access to chemical properties of Molecule atoms by atom index.
AtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty
 
AtomProperty - Class in chemaxon.struc
Class for storing atom property enumerations.
AtomProperty() - Constructor for class chemaxon.struc.AtomProperty
 
AtomProperty.MoleculeAtomProperty - Class in chemaxon.marvin.space
 
AtomProperty.Radical - Enum in chemaxon.struc
Enumeration of the supported radicals.
AtomProperty.SmoleculeAtomProperty - Class in chemaxon.marvin.space
 
AtomQueryPropertyChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms having an query property set.
AtomQueryPropertyChecker() - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.
AtomQueryPropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
Creates a new AtomQueryPropertyChecker instance to detect the given query properties.
AtomQueryPropertyCheckerResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying atom query properties, thus errorType property is StructureCheckerErrorType.ATOM_QUERY_PROPERTY by default.
AtomQueryPropertyCheckerResult(StructureChecker, List<MolAtom>, Molecule, String, List<String>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
Constructor which initialize all the properties.
atoms() - Method in class chemaxon.struc.MoleculeGraph
Provides a list view of the atoms in the molecule.
AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters
Selection which contains atom indexes.
AtomSelection(List<Integer>, List<Integer>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Constructs an AtomSelection from lists.
AtomSelection(int[], int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated.
AtomSelection(int, int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
Deprecated.
atomSet - Variable in class chemaxon.struc.Sgroup
Set for storing the atoms of the s-group's graph.
ATOMSIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of atom label font size parameter.
ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants
Either stereo atom type.
ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants
Stereo atom type mask.
ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants
No stereo atom type specified.
ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants
Specific stereo atom type.
AtomTypeChecker - Class in chemaxon.checkers
A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.
AtomTypeChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomTypeChecker
Parameterized constructor providing the possibility for descendants to initialize with their own error type.
AtomTypeChecker() - Constructor for class chemaxon.checkers.AtomTypeChecker
Default constructor.
AtomTypeChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomTypeChecker
Parameterized constructor.
atomTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
atomTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether atom types should be considered in search.
atomTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
AtomValueChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting atoms with atom value.
AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker
Default constructor.
ATPROP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom properties flag.
AtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop
Filter for atrop stereo centers.
AtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
 
AtropisomerChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting atropisomers in the molecule.
AtropisomerChecker() - Constructor for class chemaxon.checkers.AtropisomerChecker
Initializes the atropisomer structure checker
AtropIsomerDetector - Class in chemaxon.marvin.alignment
Molecular mechanics based atropisomer detection.
AtropIsomerDetector() - Constructor for class chemaxon.marvin.alignment.AtropIsomerDetector
 
AtropIsomerDetector.Accuracy - Enum in chemaxon.marvin.alignment
 
AtropStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Atrop stereo center implementation.
AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Constructs a new instance of axial stereo center with attached data.
AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Constructs a new instance of axial stereo center.
AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Deprecated.
AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
Deprecated.
atropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the atrop stereocenters.
atropStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the atrop stereocenters with attached data.
AtropStereoDescriptor - Class in chemaxon.struc
Descriptor representing atrop stereo information, the rotation of two aromatic rings connected by a single bond (axis), and at least 3 of the ligands in the ring connected to the axis has a non-ring ligand. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.ODD means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.EVEN means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is counter-clockwise. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.UNKNOWN means that it can not be decided if it is clockwise or counter-clockwise, but there is no wiggly bond - like a 2D structure without wedge information.. CIPStereoDescriptorIface.CIPValue.AtropStereoValue.WIGGLY means that there is a wiggly bond on either ligand in the ring connected to the axis, or the axis is wiggly.
AtropStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AtropStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AtropStereoDescriptor
 
ATSYM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show atom symbols in 3D flag.
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.
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
ATTACHED_DATA_MATCH_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact match of attached data.
ATTACHED_DATA_MATCH_GENERAL - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for general match of attached data.
ATTACHED_DATA_MATCH_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignoring attached data.
AttachedData - Class in com.chemaxon.calculations.stereoanal.stereocenters
Data object which contains a name and a data (String).
AttachedData(String, String) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
Creates an AttachedData class.
AttachedDataChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting attached data in the molecule.
AttachedDataChecker() - Constructor for class chemaxon.checkers.AttachedDataChecker
Default constructor
ATTACHMENT_ATOM - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.
ATTACHMENT_LABEL - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...
ATTACHMENT_MAP - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int).
ATTACHMENT_NONE - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: none (no attachment point data).
ATTACHMENT_POINT - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: R-group attachment.
ATTACHMENT_RLABEL - Static variable in interface chemaxon.sss.SearchConstants
Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String).
Au - Static variable in class chemaxon.core.ChemConst
 
AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Automatic check for structures.
AUTO_RESOLUTION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
AUTO_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "autoscale".
AUTO_TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "autoTabScale".
AUTO_UNGROUP - Static variable in class chemaxon.struc.MoleculeGraph
Automatic ungroup bit in flags.
autoGzip(InputStream) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Detect gzipped InputStream.
AutoMapper - Class in com.chemaxon.mapper
AutoMapper is a tool that performs automated chemical reaction mapping.
AutoMapper() - Constructor for class com.chemaxon.mapper.AutoMapper
Initializes an AutoMapper object
AutoMapper.Options - Class in com.chemaxon.mapper
Option object for set common options when mapping called by static way.
AUTOMATIC_FOG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated. 
AUTOMATIC_FOG_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "automaticFogEnabled".
AUTOMATIC_REACTION_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "automaticReactionEnabled".
automaticSettingOfGridSize - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat
Image object (java.awt.Image).
AxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial
Filter for axial stereo centers.
AxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
 
AxialStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Axial stereo center implementation.
AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Constructs a new instance of axial stereo center with attached data.
AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Constructs a new instance of axial stereo center.
AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Deprecated.
AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
Deprecated.
axialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the axial stereocenters.
axialStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the axial stereocenters with attached data.
AxialStereoDescriptor - Class in chemaxon.struc
 
AxialStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AxialStereoValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AxialStereoDescriptor
 

B

B - Static variable in class chemaxon.core.ChemConst
 
B_FACTOR_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
Ba - Static variable in class chemaxon.core.ChemConst
 
BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "background".
BACKGROUND_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
 
BACKGROUND_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColor - Variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
backgroundColorMode - Variable in class chemaxon.marvin.space.monitor.Label
 
BACKGROUNDLOAD_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bgloadEnabled".
BACKGROUNDLOAD_PRIORITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bgload".
balabanIndex() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "ballRadius".
ballPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
ballRadius(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the ball radius in ball and stick mode.
BALLRADIUS - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Ball radius for ball and stick mode.
ballRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BALLSTICK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
use RenderingStyle instead.
BALLSTICK_RENDERING_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
use RenderingStyle instead.
BASE64 - Static variable in class chemaxon.formats.MFileFormat
BASE64 encoded file.
BASIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
Constant denoting basic pKa.
Be - Static variable in class chemaxon.core.ChemConst
 
beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
Changes the cursor to hourglass at the beginning of a long operation.
bgColor(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the background color.
bgColorAlpha(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the background color with alpha value.
Bh - Static variable in class chemaxon.core.ChemConst
 
Bi - Static variable in class chemaxon.core.ChemConst
 
Bk - Static variable in class chemaxon.core.ChemConst
 
BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Constant storing the blue rgb value (the basic pKa result color).
BOLD - Static variable in class chemaxon.struc.graphics.MFont
Bold font style.
BOLD - Static variable in class chemaxon.struc.MolBond
"Bold" attribute of the bond.
BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "boldBondWidth".
BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bold bond width parameter.
bond - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
BOND_BOND_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
This String represents the key of cloned bond, original bond map
BOND_DRAGGED_ALONG - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "bondDraggedAlong".
BOND_DRAW_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_FACING - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondHashSpacing".
BOND_HASH_SPACING - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bondHashSpacing parameter.
BOND_LENGTH - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondLength".
BOND_LENGTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bond length parameter.
BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondLengthVisible".
BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show bond lengths.
BOND_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "bondSet".
BOND_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondSetColor".
BOND_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "bondSpacing".
BondAngleChecker - Class in chemaxon.checkers
Bond Angle Checker detects wrong bond angles in 2D structures.
BondAngleChecker() - Constructor for class chemaxon.checkers.BondAngleChecker
Default constructor
BondAngleChecker(double) - Constructor for class chemaxon.checkers.BondAngleChecker
Deprecated.
Not used.
BondAngleCheckerResult - Class in chemaxon.checkers.result
Bond angle checker result.
BondAngleCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongAngleBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondAngleCheckerResult
Constructor which initialize all the properties.
BondAngleFixer - Class in chemaxon.fixers
Bond Angle Fixer fixes wrong bond angles in 2D structures.
BondAngleFixer() - Constructor for class chemaxon.fixers.BondAngleFixer
 
BondChecker - Class in chemaxon.checkers
Descentants of the abstract BondChecker class detect bond related problems.
BondChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.BondChecker
Constructor to create a Structure checker instance with the given errorType.
bondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the number of bonds in the molecule including bonds of implicit hydrogens.
bondCount - Variable in class chemaxon.struc.MolAtom
Number of bonds.
bondCount - Variable in class chemaxon.struc.MoleculeGraph
The number of bonds.
bondDistance - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bondFacing - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bondHashSpacing() - Method in class chemaxon.marvin.io.image.ImageExporter
 
bondHashSpacing(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
The spacing of the hash in hashed bonds in C-C bond length units.
BondInfo - Class in chemaxon.marvin.alignment.atrop
Encapsulates bond info.
BondInfo(int, int, int) - Constructor for class chemaxon.marvin.alignment.atrop.BondInfo
Construct.
BondIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.BondIterator
Constructs an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.
BONDLEN_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Show bond lengths flag.
bondlength() - Method in class chemaxon.struc.Molecule
Calculate the regular bond length for the unified structure.
bondlength() - Method in class chemaxon.struc.MoleculeGraph
Calculates the regular bond length.
BondLengthChecker - Class in chemaxon.checkers
Bond Length Checker detects bonds with wrong length in 2D structures.
BondLengthChecker() - Constructor for class chemaxon.checkers.BondLengthChecker
Default constructor
BondLengthChecker(Map<String, String>) - Constructor for class chemaxon.checkers.BondLengthChecker
Deprecated.
Checker has no parameters.
BondLengthCheckerResult - Class in chemaxon.checkers.result
Bond angle checker result.
BondLengthCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongLengthBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondLengthCheckerResult
Constructor which initialize all the properties.
BondLengthFixer - Class in chemaxon.fixers
Bond Length Fixer fixes bonds with wrong length in 2D structures.
BondLengthFixer() - Constructor for class chemaxon.fixers.BondLengthFixer
 
BONDLIST - Static variable in class chemaxon.sss.search.MarkushFeature
Expansion type: bond list.
BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
Constructs an iterator to process the bonds connecting to the specified atom.
bondRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
 
bonds() - Method in class chemaxon.struc.MolAtom
Provides a list view of the connected bonds of the atom.
bonds() - Method in class chemaxon.struc.MoleculeGraph
Provides a list view of the bonds in the molecule.
bondSkipped(BondInfo, String) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when visited bond is skipped.
bondSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BondTable - Class in chemaxon.core.util
Provides easy lookup of bonds between pair of atoms in a molecule graph.
bondType(int) - Method in class chemaxon.calculations.TopologyAnalyser
Determines the type of a bond (aromatic bonds are automatically recognized)
bondTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
bondTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether bond types should be considered in search.
bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom
Calculates the average of the bond unit vectors pointing out of this atom.
bondWidth(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the width of the double bond.
BONDWIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Prefix of bond width parameter.
bondWidth - Variable in class chemaxon.marvin.space.MoleculeComponent
 
BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor
Boolean option.
booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp
Gets the boolean value.
BORDER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "border".
BORDER_MODE_BRIGHTER_FOREGROUND - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_FOREGROUND_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
 
BORDER_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
 
borderColor - Variable in class chemaxon.marvin.space.monitor.Label
 
borderColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
 
borderColorMode - Variable in class chemaxon.marvin.space.monitor.Label
 
BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
BoundingBox - Class in chemaxon.marvin.space
Class for representing a bounding box of any component in the 3D space.
BoundingBox() - Constructor for class chemaxon.marvin.space.BoundingBox
Creates a new instance of BoundingBox but does not set anything.
BoundingBox(float, float, float, float, float, float) - Constructor for class chemaxon.marvin.space.BoundingBox
Creates a bounding box with the given coordinates, computes the center and radius of the box.
boundingBox - Variable in class chemaxon.marvin.space.GraphicComponent
The smallest box containing the graphic component.
Br - Static variable in class chemaxon.core.ChemConst
 
brackets - Variable in class chemaxon.struc.Sgroup
 
BracketsChecker - Class in chemaxon.checkers
Detects brackets (S-groups) in molecules.
BracketsChecker() - Constructor for class chemaxon.checkers.BracketsChecker
Default constructor.
BRIDGEHEAD_H - Static variable in class chemaxon.struc.MolAtom
Hydrogen atom which is connected to a bridgehead atom.
btab - Variable in class chemaxon.struc.MoleculeGraph
Bond table.
bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream
Reads a character and writes into the buffer.
build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
 
build() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
Builds a ValenceCheckOptions object.
build() - Method in class chemaxon.formats.MolConverter.Builder
Builds the MolConverter.
build() - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
build() - Method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.exporter.JpegExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.exporter.PngExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Builds an unmodifiable export option.
build() - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
build() - Method in interface com.chemaxon.apidiscovery.interfaces.ParameterBuilder
Constructs an immutable instance of T.
build() - Method in class com.chemaxon.search.MatchingOptions.Builder
Creates a search options object with the settings specified by this builder instance.
build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder
 
Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder
 
Builder() - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
 
Builder() - Constructor for class chemaxon.formats.MolConverter.Builder
Constructs an empty Builder object.
Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder
 
builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder
 
builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder
 
builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder
 
builder() - Static method in class chemaxon.marvin.io.image.exporter.JpegExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.marvin.io.image.exporter.JpegExporter.Builder
 
builder() - Static method in class chemaxon.marvin.io.image.exporter.MsbmpExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder
 
builder() - Static method in class chemaxon.marvin.io.image.exporter.PngExporter
Creates a builder for this class.
Builder() - Constructor for class chemaxon.marvin.io.image.exporter.PngExporter.Builder
 
Builder() - Constructor for class chemaxon.marvin.io.image.ImageExporter.Builder
 
Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
 
Builder() - Constructor for class com.chemaxon.search.MatchingOptions.Builder
Creates a Builder object with the default settings.
Builder(MatchingOptions) - Constructor for class com.chemaxon.search.MatchingOptions.Builder
Creates a Builder object containing the settings of the given search options object.
Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object with the default settings.
Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
Creates a Builder object containing the settings of the given search options object.
BuilderClass - Annotation Type in com.chemaxon.apidiscovery.annotations
This annotation gives information about the associated ParameterBuilder for this class.
BuildupMcs - Class in com.chemaxon.search.mcs.buildup
Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
BuildupMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.buildup.BuildupMcs
Creates a new BuildupMcs object with the given search options.
BUILT_IN_CHAIN_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in chain colors.
BUILT_IN_CPK_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in cpk colors.
BUILT_IN_RAINBOW_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in rainbow colors.
BUILT_IN_RESIDUE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in residue colors.
BUILT_IN_SECONDARY_STRUCTURE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
Coloring by built-in secondary structure colors.
BUTTON_MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "buttonmenubar".
BYTE - Static variable in class chemaxon.naming.DocumentToStructure
 

C

C - Static variable in class chemaxon.core.ChemConst
 
C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter
Close the underlying stream.
C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter
Flush the output stream and force any buffered output bytes to be written out.
C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator
Name of the 13C chemical shift atom property.
Ca - Static variable in class chemaxon.core.ChemConst
 
CACHE_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "cacheMols".
CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for clearing all cached info.
CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in aromatization.
CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for cacheMemory.
CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in graph invariant calculation.
CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in parity calculation.
CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph
Cache removal option for remove module used in sssr.
CACHE_REMOVE_TABS - Static variable in class chemaxon.struc.MoleculeGraph
Cache remove option to clear ctab and btab.
cacheMemory - Variable in class chemaxon.struc.MoleculeGraph
 
calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates a "badness" value for the atomic coordinates.
calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the bracket endpoints from the base line of the bracket.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Calculates the geometrical center.
calcCenter() - Method in class chemaxon.struc.MDocument
Calculates the geometrical center.
calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
Calculates the geometrical center.
calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the geometrical center.
calcCenter() - Method in class chemaxon.struc.MoleculeGraph
Calculates the geometrical center.
calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
Calculates the geometrical center.
calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
Calculates the graph invariants with the assumption that hydrogens are removed.
calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the division point of a segment with a given ratio.
calcHeight() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecule height.
calcHybridization() - Method in class chemaxon.struc.MoleculeGraph
Calculates and sets hybridazation state for each atom.
calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin
Returns the logD value at fixed pH.
calcMaxDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
 
calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
Calculates the minimum distance between two atoms in the molecule.
calcOrderFromLength() - Method in class chemaxon.struc.MolBond
Calculate the bond order from the atomic distances.
calcOrderFromValence() - Method in class chemaxon.struc.MolBond
Calculate bond order from the types and charges of the two atoms.
calcOutRect() - Method in class chemaxon.struc.MoleculeGraph
Calculates the outer rectangle.
calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the outer rectangle.
calcOutRectCenter() - Method in class chemaxon.struc.MoleculeGraph
Calculates the center of the outer rectangle.
calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
Calculates the center of the outer rectangle.
CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Calculator rgb offset.
calcSimplePolymerBracket(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
Calculates the points of a simple polymer bracket that belongs to a bond.
calcStereo2() - Method in class chemaxon.struc.MolBond
Computes the stereochemistry of the bond based on the atomic coordinates.
calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
Computes the stereochemistry of the bond based on the atomic coordinates.
calcStereo2(MolAtom, MolAtom, MolAtom, MolAtom) - Static method in class chemaxon.struc.MolBond
Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates.
calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
Calculates NMR spectrum for the given input molecule.
calculate(Molecule) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculate(Molecule, SubProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculate(Molecule, SubProgressObserver, DihedralScanListener) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
Run the atropisomer calculation.
calculate() - Method in class chemaxon.marvin.alignment.MMPAlignment
Runs the MCS alignment calculation on the two structures of the constructor.
calculate(int[]) - Method in class chemaxon.util.MolAligner
Calculate best alignment based on the hit map
calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator
 
calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator
 
calculate(Molecule, Molecule, McsSearchOptions) - Method in interface com.chemaxon.search.mcs.upperbound.UpperBoundCalculator
Returns an upper bound for the number of bonds the Maximum Common Substructure of the given molecules may contain.
calculateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.
calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
 
calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.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.CIPStereoRecognizer
 
calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Calculates the coordinates during expand and contract.
calculateCosAFromScalarMul(MolBond, MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.
calculateIntrinsicSolubility(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates intrinsic solubility.
calculatePhDependentSolubility(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates pH-dependent solubility.
calculatePhDependentSolubility(Molecule, double[]) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates pH-dependent solubilities.
calculatePhDependentSolubility(Molecule, double, double, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
Calculates pH-dependent solubilities.
calculateSimilarityUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.
calculateUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.
CALCULATIONS_PACK - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Calculations Pack
CalculatorPlugin - Class in chemaxon.marvin.plugin
Common base class for calculator plugins.
CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin(Function<Molecule, Boolean>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin(Function<Molecule, Boolean>, Function<Molecule, Boolean>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
Constructor.
CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin
 
CalculatorPluginDisplay - Class in chemaxon.marvin.plugin
Common base class for calculator plugin displays.
CalculatorPluginDisplay() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginDisplay
 
CalculatorPluginOutput - Class in chemaxon.marvin.plugin
Class providing plugin output in table form.
CalculatorPluginOutput() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
Default constructor.
CalculatorPluginOutput(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
Constructor that sets plugin.
calcWidth() - Method in class chemaxon.struc.MoleculeGraph
Calculates the molecule width.
call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
Performs the calculation and returns the result returned by PluginWorkUnit.getResult().
call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
Performs the calculation and returns the result returned by ReusablePluginWorkUnit.getResult().
call() - Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnit
Performs the work unit tasks in a linear fashion, one after the other.
callback(String, Object) - Method in interface chemaxon.jep.ChemContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.jep.ChemJEP
Delegates CallbackIface.callback(String, Object) to the context.
callback(String, Object) - Method in class chemaxon.jep.context.AtomContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.jep.context.MolContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.jep.context.ReactionContext
Implements CallbackIface.
callback(String, Object) - Method in class chemaxon.marvin.space.GraphicScene
 
callback(String, Object) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
callback(String, Object) - Method in class chemaxon.marvin.space.MSpaceEasy
Callback function to make avoiding direct calls easier.
callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
Performs thread-safe asynchronous service call.
callService(DT, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
Performs a service call.
CAN_BE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
Deprecated.
Line can be in the given format.
CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
Deprecated.
Line can be in the given format.
canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
Tests whether a string can be one-letter-abbreviated peptide name.
A valid name contains only uppercase letters.
canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
Deprecated.
Tests whether a string can be three-letter-abbreviated peptide name.
canBeCT(int, int) - Method in class chemaxon.struc.MoleculeGraph
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
canBeCT(int, int, boolean) - Method in class chemaxon.struc.MoleculeGraph
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
canBeCT(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Determines whether the given bond 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.
canBeReactionComponent() - Method in class chemaxon.struc.Molecule
Tests whether an object of this class can be a reaction component.
canBeReactionComponent() - Method in class chemaxon.struc.RgMolecule
Tests whether an object of this class can be a reaction component.
canBeReactionComponent() - Method in class chemaxon.struc.RxnMolecule
Tests whether an object of this class can be a reaction component.
canBeSMARTS(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated.
Tests whether a string can be SMARTS.
canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
Deprecated.
Tests whether a string can be SMILES.
cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner
Stops the background thread
cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment
Cancel the ongoing calculation
cancel() - Method in interface chemaxon.util.Cancelable
 
Cancelable - Interface in chemaxon.util
Represents a task/operation that can be cancelled.
CancelObserver - Interface in com.chemaxon.calculations.common
Callback to propagate cancel requests into long running tasks.
canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
 
canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.
carboaliphaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
carboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.carboaliphaticRingCount()
carboaromaticRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
carboaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.carboaromaticRingCount()
CARBON_VIS_INCHAIN - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility is switched on in chain.
CARBON_VIS_INCHAIN_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
String constant for switching on carbon-visibility in chain.
CARBON_VIS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility mask.
CARBON_VIS_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility is switched off.
CARBON_VIS_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
String constant for switching off carbon-visibility.
CARBON_VIS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility offset.
CARBON_VIS_ON - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Carbon-visibility is switched on.
CARBON_VIS_ON_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
String constant for switching on carbon-visibility.
CARBON_VIS_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Array of carbon-visibility styles.
carbonDisplay(ImageExporter.CarbonDisplay) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Show the atom labels on carbon atoms.
carboRingCount() - Method in class chemaxon.calculations.Ring
Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).
carboRingCount(int) - Method in class chemaxon.calculations.Ring
Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
carboRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.carboRingCount()
carboRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.carboRingCount(int)
carboRings() - Method in class chemaxon.calculations.Ring
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
carboRings(int) - Method in class chemaxon.calculations.Ring
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
carboRings() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.carboRings()
carboRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.carboRings(int)
CARTRIDGE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: JChem Cartridge
CATIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
CCLENGTH - Static variable in class chemaxon.struc.MolBond
Default bond length.
Cd - Static variable in class chemaxon.core.ChemConst
 
CDX - Static variable in class chemaxon.formats.MFileFormat
ChemDraw CDX file.
CDXML - Static variable in class chemaxon.formats.MFileFormat
ChemDraw CDXML file.
Ce - Static variable in class chemaxon.core.ChemConst
 
CELL - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "cell".
CELL_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
CellOrComponentId - Class in chemaxon.marvin.space
Class to identify cells and components.
CellOrComponentId(int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
Creates a cell id.
CellOrComponentId(int, int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
Creates an id.
CELLSIZE - Static variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
The default viewer cell size.
center - Variable in class chemaxon.marvin.space.monitor.Control
 
center - Variable in class chemaxon.marvin.space.monitor.DihedralControl
 
centerx() - Method in class chemaxon.marvin.space.BoundingBox
Returns the x coordinate of the center of the box.
centery() - Method in class chemaxon.marvin.space.BoundingBox
Returns the y coordinate of the center of the box.
centerz() - Method in class chemaxon.marvin.space.BoundingBox
Returns the z coordinate of the center of the box.
centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane
Puts the molecule into the center of the display.
Cf - Static variable in class chemaxon.core.ChemConst
 
CFNS - Static variable in class chemaxon.jep.context.AtomContext
The context function names.
CFNS - Static variable in class chemaxon.jep.context.ReactionContext
The context function names.
chainAtomCount() - Method in class chemaxon.calculations.Ring
Calculates the number of chain atoms in the molecule excluding hydrogens.
chainAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.chainAtomCount()
chainBondCount() - Method in class chemaxon.calculations.Ring
Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.
chainBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Ring.chainBondCount()
chainTransformers(Transformer...) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a chain transformer.
chainTransformers(List<Transformer>) - Static method in class com.chemaxon.search.transformation.TransformerFactory
Returns a chain transformer.
changeColorMapperColors(int) - Method in class chemaxon.marvin.space.SurfaceColoring
Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.
CHARACTER - Static variable in class chemaxon.naming.DocumentToStructure
The starting character offset since the beginning of the document, for text formats (html, xml, txt).
charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
Gets a character of the document.
CHARGE_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Sets the circled charge's font.
CHARGE_FONT_SIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Sets the circled charge's font.
CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).
CHARGE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).
CHARGE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
Option value constant for ignore charge searching (charge information is ignored during searching).
CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup
Charge is located on atoms and displayed on atoms.
CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup
Charge is located on atoms but displayed on the whole group (bracket).
CHARGE_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Charge Plugin Group
CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "chargeWithCircle".
CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show charge symbols in a circle.
CHARGE_WITH_CIRCLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
 
CHARGE_WITH_CIRCLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
 
CHARGED_H - Static variable in class chemaxon.struc.MolAtom
Include charged Hydrogen atom(s).
chargeFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Font type in circled charge display.
chargeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
chargeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether formal charges of the atoms should be considered in search.
chargeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
ChargePlugin - Class in chemaxon.marvin.calculations
Plugin class for partial charge calculation.
ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin
Constructor.
check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
 
check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
 
check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
 
check(Molecule, 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, E) - Method in class chemaxon.checkers.ComponentChecker
Checks if the component with index i has problem
check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker
Examines if the bond is a crossed double bond.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker
 
check(Molecule) - Method in class chemaxon.checkers.InvalidChecker
 
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, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker
Detects bond of the molecule is crossing another bond or closer than the limit distance.
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, MolBond) - Method in class chemaxon.checkers.QueryBondChecker
 
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, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker
 
check() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
check() - Method in interface chemaxon.checkers.runner.CheckerRunner
Invoke a background thread which will run all checkers on the given molecule
check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker
 
check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker
 
check(Molecule) - Method in interface chemaxon.checkers.StructureChecker
Detects a specific error in the molecule.
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker
 
check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker
 
check(Molecule) - Method in interface chemaxon.jep.MolCondition
Deprecated.
Returns true if molecule should be processed, false otherwise.
check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
 
check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker
Determines if a non chiral molecule contains a chiral flag.
check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker
Determines if all asymmetric centers have absolute stereo configuration
check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
This method contains the current checking mechanism.
check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker
 
check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker
Detects attached data in the molecule
check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker
 
check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker
 
check1(Molecule) - Method in class chemaxon.checkers.BracketsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker
Determines if a non chiral molecule contains a chiral flag.
check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker
Iterates through the components and checks every component.
check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
Detects implicitizable hydrogen atoms.
check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.IncorrectTetrahedralStereoChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker
Detects if molecule has charge
check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker
 
check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker
 
check1(Molecule) - Method in class chemaxon.checkers.NonStandardWedgeSchemeChecker
 
check1(Molecule) - Method in class chemaxon.checkers.NonStereoWedgeBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RatomChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RgroupBridgeRatomChecker
 
check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.SolventChecker
 
check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker
 
check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker
 
check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker
 
check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker
 
check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker
 
check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker
Deprecated.
In version 15.8.3 the checker logic was replaced with the logic implemented in Molecule's stereoClean() method.
check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker
 
check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker
 
checkAndWait() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
 
checkAndWait() - Method in interface chemaxon.checkers.runner.CheckerRunner
Execute all the checker instances on the given molecule and return a List of StructureCheckerResult which contains all the identified problems
checkAtno(int) - Static method in class chemaxon.struc.MolAtom
Check if the given atomic number is positive and less then atomic type maximum value.
checkBondConsistency() - Method in class chemaxon.struc.MoleculeGraph
 
checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule
Empty implementation, bond consistency is not checked in case of selections.
checkBondConsistency() - Method in class chemaxon.struc.Sgroup
 
checkBonds(MolAtom) - Method in class chemaxon.struc.Sgroup
Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
checkBonds(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
checkConsistency() - Method in class chemaxon.struc.Molecule
Deprecated.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistency() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistency() - Method in class chemaxon.struc.RgMolecule
Deprecated.
As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.
checkConsistencyInEmbeddings() - Method in class chemaxon.struc.Sgroup
Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.
CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
ChemAxon's default checker configuration file name
CheckerInfo - Annotation Type in chemaxon.checkers
This annotation is responsible for adding GUI based meta data for StructureChecker implementations
CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark
 
CheckerRunner - Interface in chemaxon.checkers.runner
The descendant of CheckerRunner interface has to provide the functionality to run StructureChecker instances automatically
on the given molecule and fix the problems with the associated StructureFixer instances.

Example:

CheckerRunner can be used directly with the checkAndWait method.
CheckerSeverity - Enum in chemaxon.checkers
This enum defines the constants which represent the severity of the StructureChecker implementations
checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
 
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
 
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
Checks the input molecule.
checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Checks the input molecule.
checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.
checkSgroupConsistency() - Method in class chemaxon.struc.Molecule
Checks the internal consisitency of S-groups.
checkSgroupConsistency() - Method in class chemaxon.struc.RgMolecule
Checks the consistency of S-groups.
checkSgroupConsistency() - Method in class chemaxon.struc.RxnMolecule
Checks the consistency of S-groups.
checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.Sgroup
Checks whether the parameter s-group contains the atoms of this s-group.
checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup.
checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Checks result types.
checkValence(MoleculeGraph) - Method in enum chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
 
checkValence(MolAtom) - Method in enum chemaxon.struc.MoleculeGraph.ValenceCheckState
Deprecated.
 
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline
Is it a valid object in the document?
checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject
Is it a valid object in the document?
CHEM_CURATOR_COMPOUND - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Compound
CHEM_CURATOR_FULL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Markush
CHEM_CURATOR_VIEWER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemCurator Viewer
chemaxon.calculations - package chemaxon.calculations
Contains chemical computation modules.
chemaxon.calculations.cip - package chemaxon.calculations.cip
 
chemaxon.calculations.clean - package chemaxon.calculations.clean
 
chemaxon.calculations.dipole - package chemaxon.calculations.dipole
 
chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize
 
chemaxon.calculations.nmr - package chemaxon.calculations.nmr
 
chemaxon.calculations.nmr.io - package chemaxon.calculations.nmr.io
 
chemaxon.calculations.stereo - package chemaxon.calculations.stereo
 
chemaxon.checkers - package chemaxon.checkers
Structure checkers can be used to filter drawing mistakes or special structural elements.
chemaxon.checkers.result - package chemaxon.checkers.result
This package is used to identify problems found in molecules.
chemaxon.checkers.runner - package chemaxon.checkers.runner
This package supports the automatic running of structure checkers.
chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader
Extension package of the automatic runner functionality.
chemaxon.common.util - package chemaxon.common.util
 
chemaxon.core - package chemaxon.core
 
chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo
 
chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck
 
chemaxon.core.util - package chemaxon.core.util
 
chemaxon.fixers - package chemaxon.fixers
Structure fixers can be used to fix problems identified by structure checker instances.
chemaxon.formats - package chemaxon.formats
Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.
chemaxon.formats.recognizer - package chemaxon.formats.recognizer
Provides classes to recognize files of various file formats.
chemaxon.jep - package chemaxon.jep
Chemical Terms Evaluator classes.
chemaxon.jep.context - package chemaxon.jep.context
Specific chemical terms evaluation contexts.
chemaxon.license - package chemaxon.license
Classes related licenses, license handling, validating, GUI and documentation.
chemaxon.marvin - package chemaxon.marvin
Contains utility classes for rendering molecules.
chemaxon.marvin.alignment - package chemaxon.marvin.alignment
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
chemaxon.marvin.alignment.atrop - package chemaxon.marvin.alignment.atrop
Utilities for AtropIsomerDetector.
chemaxon.marvin.beans - package chemaxon.marvin.beans
Provides bean classes for creating Marvin based user interface.
chemaxon.marvin.calculations - package chemaxon.marvin.calculations
Provides specific plugin, plugin loader and table form output implementations.
chemaxon.marvin.common - package chemaxon.marvin.common
Contains a class for handling user settings.
chemaxon.marvin.io - package chemaxon.marvin.io
Provides classes for molecule import and export through data streams.
chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats
Core package of any import/export module.
chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (ChemAxon) compressed molfile.
chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles
 
chemaxon.marvin.io.formats.vectgraphics - package chemaxon.marvin.io.formats.vectgraphics
 
chemaxon.marvin.io.image - package chemaxon.marvin.io.image
 
chemaxon.marvin.io.image.exporter - package chemaxon.marvin.io.image.exporter
 
chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.
chemaxon.marvin.paint - package chemaxon.marvin.paint
Defines display options constants.
chemaxon.marvin.paint.constants - package chemaxon.marvin.paint.constants
 
chemaxon.marvin.plugin - package chemaxon.marvin.plugin
Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.
chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent
Classes to achieve concurrent processing of calculator plugins.
chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
Calculator plugin common GUI classes.
chemaxon.marvin.services - package chemaxon.marvin.services
Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.
chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice
 
chemaxon.marvin.services.json - package chemaxon.marvin.services.json
 
chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice
 
chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap
 
chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice
 
chemaxon.marvin.sketch - package chemaxon.marvin.sketch
Contains the sketcher's core classes and various sketching modes.
chemaxon.marvin.sketch.swing.modules.documentstyle - package chemaxon.marvin.sketch.swing.modules.documentstyle
 
chemaxon.marvin.space - package chemaxon.marvin.space
Contains the core classes of MarvinSpace including the graphic canvas and the basic visualizer classes.
chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
chemaxon.marvin.util - package chemaxon.marvin.util
Contains some utilities for example for molecule cleaning and Swing.
chemaxon.marvin.util.codeassist - package chemaxon.marvin.util.codeassist
 
chemaxon.marvin.view - package chemaxon.marvin.view
Control records in MarvinView.
chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing
Swing support for MarvinView tables.
chemaxon.naming - package chemaxon.naming
Document to Structure and Name to Structure conversion.
chemaxon.naming.document.annotate - package chemaxon.naming.document.annotate
 
chemaxon.sss - package chemaxon.sss
 
chemaxon.sss.screen - package chemaxon.sss.screen
 
chemaxon.sss.search - package chemaxon.sss.search
 
chemaxon.sss.search.options - package chemaxon.sss.search.options
 
chemaxon.struc - package chemaxon.struc
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3.
chemaxon.struc.graphics - package chemaxon.struc.graphics
Contains graphics MDocument elements.
chemaxon.struc.prop - package chemaxon.struc.prop
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
chemaxon.struc.sgroup - package chemaxon.struc.sgroup
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4.
chemaxon.util - package chemaxon.util
Provides general utility classes.
chemaxon.util.concurrent - package chemaxon.util.concurrent
Provides utility classes for concurrent processing.
chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
Provides utility classes for concurrent processing in Marvin.
chemaxon.util.concurrent.processors - package chemaxon.util.concurrent.processors
Provides utility classes for concurrent processing.
chemaxon.util.iterator - package chemaxon.util.iterator
Provides iterator classes for molecules and their components.
ChemConst - Class in chemaxon.core
 
ChemConst() - Constructor for class chemaxon.core.ChemConst
 
ChemContext - Interface in chemaxon.jep
Interface of expression evaluation contexts.
ChemJEP - Class in chemaxon.jep
Expression parser and evaluator for chemical expressions.
ChemJEP() - Constructor for class chemaxon.jep.ChemJEP
Constructor.
ChemJEP(Class) - Constructor for class chemaxon.jep.ChemJEP
Constructor.
CHEMLOCATOR_PERSONAL - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemLocator Personal
CHEMLOCATOR_SERVER - Static variable in class chemaxon.license.LicenseManager
Identifier of product: ChemLocator Server
CHINESE_NAME_TO_STRUCTURE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Chinese Name to Structure
chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
Calculates the number of chiral centers.
chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Stereochemistry.chiralCenterCount()
chiralCenterCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
Calculates the number of tetrahedral stereogenic centers.
chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry
Determines the chiral center atoms.
chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser
Deprecated.
as of release 5.5, replaced by Stereochemistry.chiralCenters()
ChiralFlagChecker - Class in chemaxon.checkers
Implementation of AbstractStructureChecker detecting "absolute stereo flag" on molecule.
ChiralFlagChecker() - Constructor for class chemaxon.checkers.ChiralFlagChecker
Constructs ChiralFlagChecker instance
ChiralFlagErrorChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).
ChiralFlagErrorChecker() - Constructor for class chemaxon.checkers.ChiralFlagErrorChecker
Default constructor
CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants
Axially chiral atom with M configuration.
CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants
Chirality mask in flags.
CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants
Axially chiral atom with P configuration.
CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants
Chiral atom of R configuration.
CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants
Pseudo-asymmetric chiral atom of r configuration.
CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants
Chiral atom of S configuration.
CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants
Pseudo-asymmetric chiral atom of s configuration.
CHIRALITY_SUPPORT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "chiralitySupport".
chiralityDisplay(ImageExporter.ChiralityDisplayOption) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the chirality display option.
CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants
R/S shown always.
CHIRALITYSUPPORT_ALL_POSSIBLE - Static variable in interface chemaxon.struc.StereoConstants
R/S shown always and highlight possible chiral centers as well.
CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants
R/S not shown for any molecule.
CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants
R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.
CIPStereoCalculator - Class in chemaxon.calculations.cip
Stereo calculator with the Cahn, Ingold, Prelog priority rules.
CIPStereoCalculator() - Constructor for class chemaxon.calculations.cip.CIPStereoCalculator
 
CIPStereoDescriptorIface - Interface in chemaxon.struc
Cahn-Ingold-Prelog (CIP) stereodescriptor interface.
CIPStereoDescriptorIface.CIPType - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue - Interface in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AtropStereoValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.AxialStereoValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.CisTransStereoValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue - Enum in chemaxon.struc
 
CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue - Enum in chemaxon.struc
 
CIPStereoRecognizer - Class in chemaxon.core.calculations.stereo
Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial, cis/trans and atrop stereo features.
CIPStereoRecognizer() - Constructor for class chemaxon.core.calculations.stereo.CIPStereoRecognizer
 
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 - Static variable in interface chemaxon.struc.StereoConstants
Cis double bond.
CIS_TRANS - Static variable in interface chemaxon.struc.StereoConstants
Cis and trans double bond mask.
CisDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
Filter for CIS double bonds.
CisDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
 
cisDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the CIS double bonds.
CisTransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
Filter for cis-trans stereo centers.
CisTransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
 
cisTransDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the CIS-TRANS double bonds.
cisTransDoubleBondsWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Calculates the CIS-TRANS double bonds with attached data.
CisTransStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
Cis-trans stereo center implementation.
CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Constructs a new instance of cis-trans stereo center with attached data.
CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Constructs a new instance of cis-trans stereo center.
CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Deprecated.
CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
Deprecated.
CisTransStereoDescriptor - Class in chemaxon.struc
 
CisTransStereoDescriptor(CIPStereoDescriptorIface.CIPValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.CisTransStereoDescriptor
 
Cl - Static variable in class chemaxon.core.ChemConst
 
CLASS - Static variable in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
Property key for Service class name as String
clean(MoleculeGraph, int, String, MProgressMonitor) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates.
clean(MoleculeGraph, int, String) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates.
clean(MoleculeGraph, int) - Static method in class chemaxon.calculations.clean.Cleaner
Calculates atom coordinates.
clean(int) - Method in class chemaxon.formats.MolConverter.Builder
Enables cleaning.
clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder
Enables cleaning.
clean(int, String) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
clean(int) - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
clean(int, String, int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Clean the specified cell.
clean(int, String) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).
clean(int, String, MProgressMonitor) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
clean3d(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
clean3d(Molecule, int) - Static method in class chemaxon.marvin.alignment.MMPAlignment
Utility for preprocessing structure for alignment.
cleanAll(int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
Clean all cells.
Cleaner - Class in chemaxon.calculations.clean
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.
Cleaner() - Constructor for class chemaxon.calculations.clean.Cleaner
 
CleanFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which cleans the molecule in 2d
CleanFixer() - Constructor for class chemaxon.fixers.CleanFixer
 
CLEANING_2D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "clean2dOpts".
CLEANING_3D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "clean3dOpts".
CLEANING_DIMENSION - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "cleanDim".
CLEANING_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "cleanOpts".
cleanup() - Method in class chemaxon.marvin.space.GraphicComponent
 
cleanup() - Method in class chemaxon.marvin.space.PharmacophoreArrow
 
cleanup() - Method in class chemaxon.marvin.space.PharmacophorePoint
 
cleanup(long) - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
Cancels work currently executed under the control of this ConcurrentProcessor instance, awaits termination of associated worker threads and releases any resource this processor has reserved.
cleanup() - Method in interface chemaxon.util.concurrent.ConcurrentProcessor
Calls ConcurrentProcessor.cleanup(long) with Long.MAX_VALUE.
cleanupRemovedRgroupMember(MoleculeGraph, int) - Method in class chemaxon.struc.RgMolecule
Clean-up after R-group removal.
CleanUtil - Class in chemaxon.marvin.util
Utility methods for cleaning.
CleanUtil() - Constructor for class chemaxon.marvin.util.CleanUtil
 
clear() - Method in class chemaxon.formats.MolConverter.Builder
Clears all settings.
clear() - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
clear() - Method in interface chemaxon.jep.ChemContext
Clears the context.
clear() - Method in class chemaxon.jep.context.AtomContext
Clears the context.
clear() - Method in class chemaxon.jep.context.MolContext
Clears the context.
clear() - Method in class chemaxon.jep.context.ReactionContext
Clears the context.
clear() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Clears the display.
clear() - Method in class chemaxon.marvin.space.BoundingBox
Clears all previously set coordinate from the box.
clear() - Method in class chemaxon.marvin.space.monitor.Monitor
Deletes all items from selectedItems.
clear() - Method in class chemaxon.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.marvin.alignment.AlignmentMolecule
 
clearCachedInfo(int) - Method in class chemaxon.struc.MoleculeGraph
Deletes the cached information depending on the given options.
clearChangesInUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Used in initializing searches.
clearCheckerMarks() - Method in class chemaxon.struc.MDocument
Clears the checker marks
clearClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Clears the clipboard by creating an empty Transferable and placing it on the clipboard.
clearExtraLabel() - Method in class chemaxon.struc.MolAtom
Clears the extra label.
clearExtraLabels() - Method in class chemaxon.struc.Molecule
Clears extra atom labels.
clearForImport(String) - Method in class chemaxon.struc.Molecule
Initializes molecule for import.
clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph
Clears the bonds vector, the properties, the flags, and sets the origin coordinates to 0.
clearForImport(String) - Method in class chemaxon.struc.RgMolecule
Clear the edges vector and the properties.
clearForImport(String) - Method in class chemaxon.struc.RxnMolecule
Clear the edges vector and the properties.
clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane
Reset undo queue.
clearHits() - Method in class chemaxon.naming.DocumentExtractor
Deprecated.
Clears the list of hits.
clearLines() - Method in class chemaxon.struc.graphics.MTextBox
Clears all lines.
clearMatch() - Method in class chemaxon.sss.search.Search
Clears the extra prerequisites of the structure search specified using addMatch calls.
clearObjects() - Method in class chemaxon.struc.Molecule
 
clearObjects() - Method in class chemaxon.struc.RgMolecule
 
clearObjects() - Method in class chemaxon.struc.RxnMolecule
Deletes the graphical objects from this.
clearObjects() - Method in class chemaxon.struc.Sgroup
Clears all MObject-s that belong to this S-groups.
clearProperties() - Method in class chemaxon.struc.MolAtom
Removes all properties from this atom.
clearProperties() - Method in class chemaxon.struc.MolBond
Removes all properties from this bond.
clearProperties() - Method in class chemaxon.struc.Molecule
Clears RDfile/SDfile properties.
clearQProps() - Method in class chemaxon.struc.MolAtom
Clears query props.
clearSavedAtomIndices() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
clearSelection(int) - Method in class chemaxon.marvin.space.GraphicScene
Sets all components and parts of components to be unselected in the given cell.
clearSelections() - Method in class chemaxon.marvin.space.GraphicCell
Sets all components and parts of components to be unselected.
clearSets() - Method in class chemaxon.struc.MDocument
Clears the atomSets and the bondSets.
ClearWedgeFixer - Class in chemaxon.fixers
Clears wedges.
ClearWedgeFixer() - Constructor for class chemaxon.fixers.ClearWedgeFixer
 
CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Flag that indicates an import operation
CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Flag that indicates an export operation
CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Undefined clipboard operation state identifier
CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
Temporary property name to mark the molecule if it comes from a file via the clipboard
ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer
Facade of the Clipboard handling in Marvin.
clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Clipboard operation type.
clipSurface(BoundingBox) - Method in class chemaxon.marvin.space.SurfaceComponent
The bounding box of the surface can be used to determine 6 clipping planes and clip (do not draw) parts lying outside of the box.
clone() - Method in class chemaxon.checkers.AbstractStructureChecker
 
clone() - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
clone() - Method in class chemaxon.checkers.SubstructureChecker
 
clone() - Method in class chemaxon.core.util.BondTable
 
clone() - Method in class chemaxon.fixers.StructureFixerDescriptor
 
clone() - Method in class chemaxon.formats.MolConverter.Builder
Clones the object.
clone() - Method in class chemaxon.formats.MolConverter.Options
Deprecated.
clone() - Method in class chemaxon.sss.search.MolSearchOptions
 
clone() - Method in class chemaxon.sss.search.SearchOptions
Makes an identical copy of this SearchObject.
clone() - Method in class chemaxon.struc.CTransform3D
 
clone() - Method in class chemaxon.struc.DPoint3
Make an identical copy.
clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
clone() - Method in class chemaxon.struc.graphics.MBracket
 
clone() - Method in class chemaxon.struc.graphics.MChemicalStruct
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MEFlow
 
clone() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
clone() - Method in class chemaxon.struc.graphics.MEllipse
 
clone() - Method in class chemaxon.struc.graphics.MFont
Creates a clone.
clone() - Method in class chemaxon.struc.graphics.MMidPoint
 
clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
 
clone() - Method in class chemaxon.struc.graphics.MPolyline
 
clone() - Method in class chemaxon.struc.graphics.MRectangle
 
clone() - Method in class chemaxon.struc.graphics.MRectanglePoint
 
clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
 
clone() - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
clone() - Method in class chemaxon.struc.graphics.MTextBox
 
clone() - Method in class chemaxon.struc.MDocument
Creates a clone.
clone() - Method in class chemaxon.struc.MObject
Creates a clone.
clone() - Method in class chemaxon.struc.MolAtom
Clones the atom.
clone() - Method in class chemaxon.struc.MolBond
Make a copy of this object.
clone() - Method in class chemaxon.struc.Molecule
Makes an identical copy of the molecule.
clone() - Method in class chemaxon.struc.MoleculeGraph
Make an identical copy of the molecule.
clone() - Method in class chemaxon.struc.MPoint
 
clone() - Method in class chemaxon.struc.MPropertyContainer
Clones this object.
clone() - Method in class chemaxon.struc.prop.MBooleanProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MDoubleProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MHCoords3DProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MIntegerProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MMoleculeProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MObjectProp
Clones the object.
clone() - Method in class chemaxon.struc.prop.MStringProp
Clones the object.
clone() - Method in class chemaxon.struc.QueryBond
Make a copy of this object.
clone() - Method in class chemaxon.struc.RgMolecule
Clone the markush structure.
clone() - Method in class chemaxon.struc.RxnMolecule
Make an identical copy of the reaction structure.
clone() - Method in class chemaxon.struc.SelectionMolecule
Create a clone of this SelectionMolecule.
clone() - Method in class chemaxon.struc.sgroup.SgroupAtom
Clones the S-group superatom and it's SuperatomSgroup as well.
clone() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Clones the SuperatomSgroup (and not the Molecule).
cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
Copies the specified atoms.
cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies the specified atoms.
cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
Clones this bond.
cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.QueryBond
Clones this bond.
cloneBondTable(BondTable) - Static method in class chemaxon.core.util.BondTable
Clones the bond table.
cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MHashProp
Clones the object.
cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MListProp
Clones the object.
clonecopy(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions
Copies parameters to other.
clonecopy(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions
Copies all search options to other.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
Makes another molecule identical to this one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
Copies the specified atoms and bonds of this molecule to another one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Make another molecule identical to this one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies the specified atoms of this molecule graph to another one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Make another molecule identical to this one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Copies the specified atoms of this graph to another one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Make another molecule identical to this one.
clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Copies the specified nodes and edges of this graph to another one.
clonecopy(MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
Copies the clones of atoms and bonds of this graph to another one.
clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Copies the specified atoms and bonds of this molecule graph to another one.
clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
Copies the specified atoms and bonds of this graph to another one.
clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions
 
clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions
Copies all search options except search type to other.
clonecopyWithoutSgroups(Molecule) - Method in class chemaxon.struc.Molecule
Copies the all the contents except the S-groups into another molecule object.
cloneDocument() - Method in class chemaxon.struc.MDocument
Creates a clone.
cloneDocument() - Method in class chemaxon.struc.MSelectionDocument
Creates a clone.
cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom
Clones the S-group superatom partially.
cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker
 
cloneItem() - Method in class chemaxon.checkers.InvalidChecker
 
cloneItem() - Method in interface chemaxon.checkers.StructureChecker
Returns a clone of this StructureChecker instance
cloneLeavingGroups(SuperatomSgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
Deprecated.
as of Marvin 6.3.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
as of Marvin 6.3.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
Deprecated.
as of Marvin 6.3.
Not supported feature.
clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
Deprecated.
as of Marvin 6.3.
Not supported feature.
cloneMainMolecule() - Method in class chemaxon.struc.MDocument
Creates a clone.
cloneMainMoleculeGraph() - Method in class chemaxon.struc.MDocument
Creates a clone.
cloneMFont() - Method in class chemaxon.struc.graphics.MFont
Creates a clone.
cloneMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
cloneMolecule() - Method in class chemaxon.struc.Molecule
Deprecated.
as of Marvin 2014.09.01.0 use Molecule.clone() instead
cloneMoleculeWithDocument() - Method in class chemaxon.struc.Molecule
Makes an identical copy of the molecule and its document.
cloneMoleculeWithDocument() - Method in class chemaxon.struc.RgMolecule
 
cloneMoleculeWithDocument() - Method in class chemaxon.struc.RxnMolecule
 
cloneProp() - Method in class chemaxon.struc.MDocument.Prop
Creates a clone.
cloneProp() - Method in class chemaxon.struc.MProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MObjectProp
Clones the object.
cloneProp() - Method in class chemaxon.struc.prop.MStringProp
Clones the object.
cloneSets(MDocument) - Method in class chemaxon.struc.MDocument
Clones the atom/bond sets from doc.
cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.Sgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.Sgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.DataSgroup
Gets a new DataSgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets a new Sgroup instance.
cloneStructure() - Method in class chemaxon.struc.Sgroup
Gets the clone of the structure stored.
cloneTemporraryObjects(MDocument) - Method in class chemaxon.struc.MDocument
 
close() - Method in class chemaxon.formats.MolConverter
Closes the exporter and the output stream.
close(int) - Method in class chemaxon.formats.MolConverter
Closes the exporter.
close() - Method in class chemaxon.formats.MolExporter
Closes the MolExportModule and the underlying stream.
close(int) - Method in class chemaxon.formats.MolExporter
Closes the MolExportModule and, optionally, the underlying stream.
close() - Method in class chemaxon.formats.MolImporter
Close the underlying input stream.
close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Interrupts parsing.
close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
 
close() - Method in class chemaxon.marvin.io.MDocSource
Closes the underlying input stream(s).
close() - Method in class chemaxon.marvin.io.MolExportModule
Close the stream.
close() - Method in class chemaxon.marvin.io.MRecordImporter
Closes the input stream.
close() - Method in interface chemaxon.marvin.io.MRecordReader
Closes the input stream.
close() - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
Closes the output.
close(int) - Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
Closes the output.
close() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
 
close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
Closes the importers.
close() - Method in interface com.chemaxon.calculations.common.SubProgressObserver
Notifies that the represented task is finished and no further work will be done.
close() - Method in interface com.chemaxon.calculations.io.CloseableIterator
 
CloseableIterator<T> - Interface in com.chemaxon.calculations.io
Closeable iterator.
CloseableIterators - Class in com.chemaxon.calculations.io
Utility class.
CLOSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
Closed flag.
closeSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane
Closes the sketcher window that belongs the the specified cell.
closeWindow(int) - Method in class chemaxon.marvin.beans.MViewPane
Closes the detached viewer window of the specified cell.
closeWindows() - Method in class chemaxon.marvin.beans.MarvinPane
Closes all windows opened by this MarvinPane.
Cm - Static variable in class chemaxon.core.ChemConst
 
CmdlineUtils - Class in com.chemaxon.calculations.util
Command line related utilities.
CML - Static variable in class chemaxon.formats.MFileFormat
Chemical Markup Language.
Co - Static variable in class chemaxon.core.ChemConst
 
CodeAssistConfiguration() - Constructor for class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
 
CodeAssistFactory - Class in chemaxon.marvin.util.codeassist
Manages the creation of Chemical Terms related components, such as the Code Assist text field, toolbars, favorite and macro handling components, and validation response component.
CodeAssistFactory.CodeAssistConfiguration - Class in chemaxon.marvin.util.codeassist
Helper class for CodeAssistFactory to set up CodeAssist
codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Add mass number information to the given code.
color - Variable in class chemaxon.marvin.space.GraphicComponent
 
color - Variable in class chemaxon.marvin.space.MoleculeComponent
 
color - Variable in class chemaxon.marvin.space.SurfaceComponent
 
color3 - Variable in class chemaxon.marvin.space.SurfaceComponent
 
COLOR_MAPPER_BLUE_TO_GREEN - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in blue-cyan-green palette will be used.
COLOR_MAPPER_BLUE_TO_RED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in blue-lightgray-red palette will be used.
COLOR_MAPPER_FIRE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in "fire" palette will be used.
COLOR_MAPPER_GREEN_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in green-cyan-blue palette will be used.
COLOR_MAPPER_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in rainbow palette will be used.
COLOR_MAPPER_RED_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in red-lightgray-blue palette will be used.
COLOR_MAPPER_REVERSE_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
Built-in reverse rainbow palette will be used.
COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "colorScheme".
COLOR_SCHEMES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Array of color schemes strings.
ColorGenerator - Class in chemaxon.marvin.util
A final class which provides a static access to a color distant color creator class.
ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator
 
coloring(ImageExporter.Coloring) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Sets the coloring scheme.
coloring(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
 
COLORING_ALL - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for setting all coloring options, currently scaffold and R-groups.
COLORING_NONE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for no hit coloring.
COLORING_RGROUPS - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for R-group coloring.
COLORING_SCAFFOLD - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Constant for scaffold coloring.
COLORS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Color scheme mask in display option flags.
COLORS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Color scheme offset in display option flags.
colorType - Variable in class chemaxon.marvin.space.MoleculeComponent
 
COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "cols".
com.chemaxon.apidiscovery - package com.chemaxon.apidiscovery
API Discovery framework.
com.chemaxon.apidiscovery.annotations - package com.chemaxon.apidiscovery.annotations
Annotations used by the API Discovery framework.
com.chemaxon.apidiscovery.interfaces - package com.chemaxon.apidiscovery.interfaces
Interfaces introduced for the API Discovery framework.
com.chemaxon.apidiscovery.util - package com.chemaxon.apidiscovery.util
Various utilities.
com.chemaxon.calculations.common - package com.chemaxon.calculations.common
Common components of Calculator APIs.
com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal
API of the elemental analysis functionality.
com.chemaxon.calculations.io - package com.chemaxon.calculations.io
 
com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility
 
com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal
API of the Stereo Analysis Plugin.
com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters
Core filter classes.
com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop
Atrop stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial
Axial stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans
Cis-trans stereo filter implementations.
com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral
Tetrahedral stereo filter implementations.
com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters
Stereocenter implementations of Stereo Analysis API.
com.chemaxon.calculations.stereoisomers - package com.chemaxon.calculations.stereoisomers
 
com.chemaxon.calculations.util - package com.chemaxon.calculations.util
Various utilities used in calculations, descriptors, clustering and overlap analysis.
com.chemaxon.common.annotations - package com.chemaxon.common.annotations
 
com.chemaxon.mapper - package com.chemaxon.mapper
 
com.chemaxon.search - package com.chemaxon.search
Tools for chemical search.
com.chemaxon.search.mcs - package com.chemaxon.search.mcs
Contains classes for finding the maximum common substructure (MCS) of molecular structures.
com.chemaxon.search.mcs.buildup - package com.chemaxon.search.mcs.buildup
Contains MCS algorithm implementation based on the "build up" method.
com.chemaxon.search.mcs.maxclique - package com.chemaxon.search.mcs.maxclique
Contains MCS algorithm implementation based on the "maximum clique" method.
com.chemaxon.search.mcs.upperbound - package com.chemaxon.search.mcs.upperbound
Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.
com.chemaxon.search.transformation - package com.chemaxon.search.transformation
 
com.chemaxon.search.transformation.transformers - package com.chemaxon.search.transformation.transformers
 
com.chemaxon.version - package com.chemaxon.version
 
compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator
 
compareAtoms(int, int) - Method in class chemaxon.sss.search.MolComparator
Compares atoms of indices a1 and a2.
compareBonds(int, int) - Method in class chemaxon.sss.search.MolComparator
Compares bonds of indices b1 and b2.
compareHit(int[], int) - Method in class chemaxon.sss.search.MolComparator
Checks a partial hit during the search algorithm.
compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
Comparison method which uses the priority field for ordering.
compareTo(Object) - Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
 
compile(String) - Method in class chemaxon.jep.ChemJEP
Compiles the expression string to an inner structure.
compile(String) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, Class) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
compile(String, Class, SymbolTable) - Method in class chemaxon.jep.Evaluator
Compiles the expression, creates ChemJEP object.
component - Variable in class chemaxon.marvin.space.monitor.Control
 
COMPONENT_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
 
COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_ENTIRE - Static variable in class chemaxon.marvin.space.GraphicComponent
Indicates if the entire component is selected by picking.
COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
COMPONENT_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
 
componentBecameSelected() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if a component became selected previously.
componentBecameSelected(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if a component became selected previously in the given cell.
componentBecameUnselected() - Method in class chemaxon.marvin.space.GraphicCell
Returns true if a component became unselected previously.
componentBecameUnselected(int) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if a component became unselected previously in the given cell.
ComponentChecker<E> - Class in chemaxon.checkers
Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).
ComponentChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.ComponentChecker
Constructor to create a Structure checker instance with the given errorType.
ComponentElement - Class in chemaxon.marvin.space
Class to identify parts of GraphicComponents mainly during selection.
ComponentElement(GraphicComponent, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement of a simple (not structured) GraphicComponent.
ComponentElement(GraphicComponent, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement.
ComponentElement(GraphicComponent, int, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement of a complex (structured) GraphicComponent.
ComponentElement(GraphicComponent, int, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
Creates a new instance of ComponentElement.
ComponentElement(ComponentElement) - Constructor for class chemaxon.marvin.space.ComponentElement
Copies the given ComponentElement.
componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Hides windows if the parent frame is hidden.
componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Does nothing.
componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Does nothing.
componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MViewPane
 
componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
Shows windows if the parent frame is hidden.
CompositeInputProducer - Class in chemaxon.util.concurrent.marvin
Input producer composed of an array of input producers.
CompositeInputProducer() - Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
Constructor.
CompositeInputProducer(InputProducer[]) - Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
Constructor.
CompositeWorkUnit - Class in chemaxon.util.concurrent.marvin
Work unit composed of an array of work units, to be called in a linear fashion in a single thread, one after the other in the specified order.
CompositeWorkUnit() - Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
Constructor.
CompositeWorkUnit(WorkUnit[]) - Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
Constructor.
CompositeWorkUnitFactory - Class in chemaxon.util.concurrent.marvin
Work unit factory composed of an aray of work unit factories.
CompositeWorkUnitFactory(WorkUnitFactory[]) - Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
Constructor.
composition(int) - Method in class chemaxon.calculations.ElementalAnalyser
Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
composition() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
COMPRESS - Static variable in class chemaxon.formats.MdlCompressor
Compression flag.
computeFunctionScale() - Method in class chemaxon.calculations.nmr.NMRSpectrum
Computes the scaling factor for the unscaled NMR spectrum function.
computeFunctionScale(double, double[]) - Method in class chemaxon.calculations.nmr.NMRSpectrum
 
computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
 
computeSurface(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MSpaceEasy
Activates the container cell of the MoleculeVisualizer, and computes its Connolly surface.
computeSurface(String) - Method in class chemaxon.marvin.space.MSpaceEasy
Computes the given type of surface in the active cell of the viewer.
ConcurrentProcessor - Interface in chemaxon.util.concurrent
Executes jobs in parallel and returns their results iterator-style.
ConcurrentProcessors - Class in chemaxon.util.concurrent.processors
Creates ConcurrentProcessor instances.
CONFIDENCE - Static variable in class chemaxon.naming.DocumentToStructure
The confidence that the structure is correct.
config - Variable in class chemaxon.checkers.StructureCheckOptions
The configuration of the structure check.
CONFIG_DIR - Static variable in class chemaxon.jep.Evaluator
Default directory for storing configuration files.
ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader
This interface is provided for classes which can read the configuration of CheckerRunner.
CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "confirmTransfer".
CONFORMATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
Identifier of plugin: Conformation Plugin Group
ConformerPlugin - Class in chemaxon.marvin.calculations
Plugin class for conformer calculation.
ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin
Constructor.
CONJUGATED - Static variable in class chemaxon.struc.MolBond
Conjugation state of the bond.
connectedMode(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
Sets whether the common substructures should be connected or they can consist of multiple fragments.
connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule
 
connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
Sets the original connections to the new atom.
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
 
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
 
connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject
 
constant - Variable in class chemaxon.marvin.services.ServiceArgument
field indicates constant argument
containerFrame - Variable in class chemaxon.marvin.space.MSpaceEasy
 
contains(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
Tells whether the given location is inside the box.
contains(MObject) - Method in class chemaxon.struc.MDocument
Searches an object in the document.
contains(MDocument) - Method in class chemaxon.struc.MDocument
Tests whether the document contains all objects of another document.
contains(MolAtom) - Method in class chemaxon.struc.Molecule
Checks if the molecule graph contains the specified atom.
contains(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Checks if the molecule graph contains the specified atom.
contains(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(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(MolAtom) - Method in class chemaxon.struc.RgMolecule
Checks if the root structure or an R-group contains the specified node.
contains(MolBond) - Method in class chemaxon.struc.RgMolecule
Checks if the root structure or an R-group contains the specified edge.
contains(MolAtom) - Method in class chemaxon.struc.RxnMolecule
Checks if a reactant, agent or product structure contains the specified node.
contains(MolBond) - Method in class chemaxon.struc.RxnMolecule
Checks if a reactant, agent or product structure contains the specified edge.
contains(MolAtom) - Method in class chemaxon.struc.Sgroup
Is this atom contained by the s-group?
containsAllAtomsOf(Sgroup) - Method in class chemaxon.struc.Sgroup
Checks if the S-group contains the atoms of another S-group.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
Checks if the atom set contains the specified atom object.
containsAtom(MolAtom) - Method in class chemaxon.struc.MObject
Checks if the object contains the specified atom reference.
containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
Tells whether the component is in the cell.
containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
Returns true if the component exists in the scene.
containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule graph contains coordinate bonds.
containsLadderTypePolymer() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the structure of this sgroup contains a ladder-type repeating unit.
containsMulticenterSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule contains Multicenter S-groups.
containsOnlyOne(Class) - Method in class chemaxon.struc.MDocument
Tests whether the document contains only one object of the specified class.
containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
 
containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom
Returns true if this atom has a mapping for the specified property key.
containsPropertyKey(String) - Method in class chemaxon.struc.MolBond
Returns true if this bond has a mapping for the specified property key.
containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns true if molecule contains pseudo atom.
containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Decides whether a molecule contains SRU S-groups.
CONTEXT - Static variable in class chemaxon.naming.DocumentToStructure
The context of the structure recognized in the text.
CONTEXT_INDEX - Static variable in class chemaxon.naming.DocumentToStructure
Index of the hit inside the context.
contract(int) - Method in class chemaxon.struc.Sgroup
Sets the state to Sgroup.XSTATE_C.
contract(int) - Method in interface chemaxon.struc.sgroup.Expandable
Contracts the S-group.
contract(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
Contracts this S-group.
contract(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Contracts this S-group.
ContractGroupFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule
ContractGroupFixer() - Constructor for class chemaxon.fixers.ContractGroupFixer
 
contractOrExpandSgroups(int, String, boolean) - Method in class chemaxon.marvin.view.MDocStorage
Contract or expand S-groups in the specified cell.
contractOrExpandSgroupsAll(boolean) - Method in class chemaxon.marvin.view.MDocStorage
Contract or expand S-groups in all molecules.
contractSgroups() - Method in class chemaxon.struc.Molecule
Contracts all S-groups.
contractSgroups(int) - Method in class chemaxon.struc.Molecule
Contracts all S-groups.
Control - Class in chemaxon.marvin.space.monitor
Transformation on a GraphicComponent that changes the coordinates, and not just the view.
Control() - Constructor for class chemaxon.marvin.space.monitor.Control
Creates a new instance of Control
control(int, int) - Method in class chemaxon.marvin.space.monitor.Control
Does control on x-y events.
control(int) - Method in class chemaxon.marvin.space.monitor.Control
Does control on z event.
control(int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
One part of the molecule being in one of the end of the torsion bond will be rotated around the bond.
control(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
Does nothing.
control - Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
 
control(int) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Passes the control event to the control.
control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Changes the location say translates the component of the control in the global coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
Changes the location say translates the component of the control in the global coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Changes the orientation say rotates the component of the control in the global coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
Changes the orientation that is rotates the component of the control in the global coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Changes the location say translates the component of the control in its local coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
Changes the location say translates the component of the control in its local coordinate system.
control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Changes the orientation say rotates the component of the control in its local coordinate system.
control(int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
Changes the orientation say rotates the component of the control in its local coordinate system.
control - Variable in class chemaxon.marvin.space.monitor.Monitor
 
control(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Causes the monitor's controll to take action with 2 parameters.
control(int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Causes the monitor's controll to take action with 1 parameter.
control(int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
Resizes the component in z direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
control(int, int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
Resizes the component in x, y direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
 
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
 
convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
This method converts the entities contained in this result according to the convertData.
convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.ModeConverter
 
convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.TypeConverter
 
convert() - Method in class chemaxon.formats.MdlCompressor
Compression/decompression
convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor
(Un)compress the specified molfile or SDfile.
convert(String, int) - Static method in class chemaxon.formats.MdlCompressor
(Un)compress the specified molfile or SDfile.
convert() - Method in class chemaxon.formats.MolConverter
Convert the next molecule.
convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
 
convert(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Creates an MDL mol or compressed mol representation of the molecule.
convert(Molecule) - Method in class chemaxon.marvin.io.MolExportModule
Convert a molecule to a string or byte array.
convert(TransferDataConverter) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
Convert transfer data available on clipboard in one of the requested flavors.
convert(String) - 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
 
ConvertConstants - Class in chemaxon.checkers.result
This class contains convert relevant constants
ConvertConstants() - Constructor for class chemaxon.checkers.result.ConvertConstants
 
convertCoordinateBondsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Converts coordinate bonds to data sgroups (attached data) with field name MRV_COORDINATE_BOND.
convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert explicit Hydrogen atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert explicit Hydrogen atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.
convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.
convertExplicitLonePairsToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Converts explicit lone pairs from a molecule to implicit.
convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit Hydrogen atoms of the molecule to explicit.
convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
Convert implicit lone pairs of the atoms of a molecule to explicit.
convertPageSettingsToData(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport
Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX.
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(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(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
Deprecated.
This method converts the result by changing the atoms and bonds back to the original instead of the cloned ones
convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker
This implementation does nothing.
ConvertToAtomFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information
ConvertToAtomFixer() - Constructor for class chemaxon.fixers.ConvertToAtomFixer
 
ConvertToCarbonFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms
ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer
 
ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond
ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
 
ConvertToElementalFormFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms
ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer
 
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(MProp, String) - Static method in class chemaxon.marvin.io.MPropHandler
Converts the property to text format.
convertToString(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler
Convert key of MPropertyContainer to string.
convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop
Deprecated.
convertToString(String, int) - Method in class chemaxon.struc.MProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String) - Method in class chemaxon.struc.MProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp
Deprecated.
As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String)
ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts crossed double bond to wiggly
ConvertToWigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToWigglyDoubleBondFixer
 
convertTransform(CTransform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle
 
coordBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Coordinate bond display style.
coordBondStyleAtMulticenter(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Coordinate bond display style when it connects to a multicenter atom.
COORDDEP - Static variable in class chemaxon.struc.MProp
Coordinate dependent property.
COORDINATE - Static variable in class chemaxon.struc.MolBond
Coordinate bond flag.
COORDINATE_BOND_ARROW_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_AT_MULTICENTER_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_AT_MULTICENTER_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_AT_MULTICENTER_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_HASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_STYLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "coordinateBondStyle".
COORDINATE_BOND_STYLE_AT_MULTICENTER - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "coordinateBondStyleAtMulticenter".
COORDINATE_BOND_STYLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_STYLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
COORDINATE_BOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Deprecated.
CoordinateBondOnMulticenterStyle - Enum in chemaxon.marvin.paint.constants
Holds the values for the possible rendering styles for Coordinate bonds connected to Multicenter atoms.
CoordinateBondStyle - Enum in chemaxon.marvin.paint.constants
Holds the values for the possible rendering styles for Coordinate bonds.
CoordinationSystemErrorChecker - Class in chemaxon.checkers
Detects errors of multicenter coordination systems.
CoordinationSystemErrorChecker() - Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker
Default constructor
COORDS_UPDATE - Static variable in interface chemaxon.struc.sgroup.Expandable
Deprecated.
As of Marvin 6.2, no replacement.
Not supported feature.
COPY_AS_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
Default format to be selected on Copy as dialog.
COPY_AS_IMAGE_BITMAP - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
Deprecated. 
COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
since 5.3.3 has no sense
CopyOptConstants - Interface in chemaxon.marvin.util
Deprecated.
since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this interface either non exists in the new implementation or its value has changed. See the constants own description for details.
copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket
Copies line properties to another line object.
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow
 
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline
Copies line properties to another line object.
correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
 
countAllAtoms() - Method in class chemaxon.struc.MolAtom
Counts all atoms represented by this atom.
countAllAtoms() - Method in class chemaxon.struc.Sgroup
Counts the total number of atoms recursively.
countAllAtoms() - Method in class chemaxon.struc.sgroup.SgroupAtom
Counts all atoms represented by this atom.
countEnumerations() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the number of all enumerated structures, no arithmetic overflow because counts in BigInteger.
countEnumerationsMagnitude() - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures.
countExpandableContractableSgroups() - Method in class chemaxon.struc.Molecule
Counts the expandable and contractable S-groups.
countOrderedComponentSgroups() - Method in class chemaxon.struc.Molecule
Counts the ordered component S-groups.
countRecords(MProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.view.MDocStorage
Counts the total number of records and sets the size of the document storage.
countRecordsInFraction(double, int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
Deprecated. 
COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Covalent hydration error remark.
CovalentCounterionChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).
CovalentCounterionChecker() - Constructor for class chemaxon.checkers.CovalentCounterionChecker
Default constructor
CovalentCounterionFixer - Class in chemaxon.fixers
Deprecated.
CovalentCounterionFixer() - Constructor for class chemaxon.fixers.CovalentCounterionFixer
Deprecated.
 
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.marvin.paint.DispOptConsts
CPK color scheme in display option flags.
CPK_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
CPK color scheme.
Cr - Static variable in class chemaxon.core.ChemConst
 
crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
create(byte[]) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule
Deprecated.
create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
 
create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
 
create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
create(int, InputProducer) - Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
 
create(int, InputProducer, WorkUnitFactory) - Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
 
create(String) - Static method in class chemaxon.util.DotfileUtil
Opens a dotfile for writing.
create() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
Invoke creator method.
create() - Static method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
Constructs a new StereoisomerSettings object with default settings.
create(Molecule, Molecule) - Method in interface com.chemaxon.search.CustomMatcherFactory
Creates a custom matcher for atom and bond pairs of the given query and target molecules.
createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
Constructs an elemental analysis from molecular formula.
createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value
createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value
createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value and type
createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
Returns a service argument based on value and type
createAromatizedSearcher(AromatizationMethod) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that considers aromatization differences of the input molecule.
createAromatizedSearcher(AromatizationMethod, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher which considers aromatization according to the specified rules and initializes it with the specified search options.
createArray(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
Creates an array property.
createArrayXSD(String, String, int, int) - Static method in class chemaxon.marvin.io.MPropHandler
Creates an array property from the XSD type.
createAtomIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
createAtomNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an iterator to get the atom neighbours of the specified atom.
createBHtab() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 6.2, no replacement.
No replacement.
createBHtab() - Method in class chemaxon.struc.RxnMolecule
Creates the graph union's bond table extended with implicit hydrogen atoms.
createBondIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs a bond iterator for the specified molecule of the factory according to bond related behavior set in the factory.
createBondNeighbourIterator(MolAtom) - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an iterator to get the bonds connecting to the specified atom.
createBondTable(int, int) - Static method in class chemaxon.core.util.BondTable
Creates a new bond table for a molecule graph with the specified number of atoms and bonds.
createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
 
createChemicalTermsTextPane() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
createChemicalTermsTextPane(boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
createChemicalTermsTextPane(String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
createChemicalTermsTextPane(String, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
createChemicalTermsTextPane(String, String, boolean, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Deprecated.
use CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration) Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
Creates a JTextPane instance with code assist capabilities.
createCHtab() - Method in class chemaxon.struc.MoleculeGraph
Creates the connection table extended with implicit hydrogen atoms.
createCHtab() - Method in class chemaxon.struc.RxnMolecule
Creates the graph union's connection table extended with implicit hydrogen atoms.
createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
 
createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument
Creates a ServiceArgument constant based on string value and argument type.
Supported types are String, Integer, Long, Double, Float and Boolean
createDefaultParameterPanel(String, Component) - Static method in class chemaxon.marvin.plugin.PluginFactory
Creates default parameter panel based on XML config.
createDefaultParameterPanel(Class, String, Component) - Static method in class chemaxon.marvin.plugin.PluginFactory
 
createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph
Creates a dehydrogenized version of the molecule.
createEMF(String, String) - Static method in class chemaxon.util.ImageExportUtil
Creates a .NET based EMF picture.
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.
createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
createGData() - Method in class chemaxon.marvin.space.SurfaceComponent
 
createGearch() - Method in class chemaxon.struc.Molecule
 
createGearch() - Method in class chemaxon.struc.MoleculeGraph
 
createGearch() - Method in class chemaxon.struc.RgMolecule
 
createGearch() - Method in class chemaxon.struc.RxnMolecule
 
createGearch() - Method in class chemaxon.struc.SelectionMolecule
 
createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
 
createImage(Buffer, int, int) - Method in class chemaxon.marvin.space.GraphicScene
 
createImageExporterParameter(Properties, String, MDocument) - Static method in class chemaxon.util.ImageExportUtil
Creates the Image Exporter parameter String based on the values in the Properties object.
createImportMod(MolInputStream) - Static method in class chemaxon.marvin.io.MRecordImporter
Creates an importer for the specified molecule input stream.
createImportMod(String) - Static method in class chemaxon.marvin.io.MRecordImporter
Creates an importer for the specified molecule format.
createImportModule() - Method in class chemaxon.formats.MFileFormat
Creates the molecule import module.
createInDocumentAt(DPoint3, MDocument) - Static method in class chemaxon.struc.NoStructure
Creates a NoStructure at the given location.
createInDocumentFrom(Molecule, MDocument) - Static method in class chemaxon.struc.NoStructure
Creates a NoStructure from the given component.
createInput() - Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
 
createLicenseManagerPanel() - Static method in class chemaxon.license.LicenseManager
Creates the main panel which is used for end-user license managing.
createMatrixArray() - Method in class chemaxon.core.util.BondTable
Creates the matrix array representation.
createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
Deprecated.
as of Marvin 3.3.1, replaced by SwingUtil.createMenu
createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
Utility method to create a menu with a label specified as a resource.
createMenu(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu with a label specified as a resource.
createMenuItem(ResourceBundle, String, Class<?>, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu item 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) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a menu with a label specified as a resource.
createMessagePane(String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a message pane with HTML text content.
createMMoleculeProp(String) - Static method in class chemaxon.marvin.io.MPropHandler
 
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
Returns the major tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
Returns the molecule form with largest distribution.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
Returns the major tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
Returns the canonical tautomeric form of the molecule.
createModifiedInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Returns the modified input molecule (e.g.
createMol() - Method in class chemaxon.formats.MolImporter
Creates a target molecule object for import.
createMol() - Method in class chemaxon.marvin.io.formats.mdl.MolImport
Creates a new target molecule object.
createMol() - Method in class chemaxon.marvin.io.MolImportModule
Creates a new target molecule object for the import.
createMol() - Method in class chemaxon.marvin.io.MRecordImporter
Creates an empty target molecule for import.
createMolConverter(InputStream, OutputStream, String[], int[]) - Static method in class chemaxon.formats.MolConverter
Creates a MolConverter instance with the attributes specified in the parameters.
createMolecule() - Method in class chemaxon.struc.Sgroup
Creates a molecule object that contains only this group.
createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Creates a molecule object that contains only one SuperatomSgroup identical to this one.
createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.
createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Creates a MoleculeIterator object for iterating through collection of molecules (Molecule objects).
createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
Creates a MoleculeIterator object for iterating through a molecule array (Molecule[]).
createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter
Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.
createNeighbourBonds(Molecule, MolBond, boolean) - Static method in class chemaxon.checkers.StructureCheckerHelper
This method returns a List of MolBond which contains all bonds which are in isNeighbour relation with the MolBond instance represented by parameter bond
createNew(Molecule) - Static method in class chemaxon.marvin.alignment.MCSAlignment.Factory
Constructs a new instance of ConformationAlignment class.
createNew() - Static method in class chemaxon.marvin.calculations.HlbPlugin.Builder
Constructs a new HlbPlugin instance.
createNewCell() - Method in class chemaxon.marvin.space.GraphicScene
Sets an empty cell to be the active cell.
createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
Creates identical attributes for the next section.
createNoCancelObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers
createParameterPanel() - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Creates the parameter panel.
createPooledWu(int, InputProducer, WorkUnitFactory) - Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
For test only
createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule
Creates a reaction.
createReaction(MoleculeGraph, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
Creates a reaction.
createRecognizer() - Method in class chemaxon.formats.MFileFormat
Creates a recognizer module.
createRecognizer(String) - Method in class chemaxon.formats.MFileFormat
Deprecated.
as of Marvin 2014.07.21.0 use MFileFormat.createRecognizer() instead
createRecordReader(MolInputStream, String) - Method in class chemaxon.formats.MFileFormat
Creates the record reader.
createRecordReader(InputStream, String) - Static method in class chemaxon.formats.MFileFormatUtil
Creates a record reader for an input stream.
createRecordReader(InputStream, String, String, String) - Static method in class chemaxon.formats.MFileFormatUtil
Creates a record reader for an input stream.
createResult(Molecule, List<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<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.
createResult(Molecule, List<MolAtom>) - Method in class chemaxon.checkers.PseudoAtomChecker
 
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
createResultView(String, MolPanel) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
 
createRgComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an rgroup definition component iterator for the specified molecule of the factory if the molecule is an RgMolecule, an empty iterator otherwise.
createRotationAboutBond(MolBond, double) - Static method in class chemaxon.marvin.util.CleanUtil
Creates a rotation transformation about a bond.
createRxnComponentIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs a reaction component iterator for the specified molecule of the factory if the molecule is an RxnMolecule, an empty iterator otherwise.
createSavedCoordsArray(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
Creates an empty array for the atomic coordinates of a structure.
createScalar(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
Creates a scalar property.
createScalar(String, String, MProgressMonitor) - Static method in class chemaxon.marvin.io.MPropHandler
Creates a scalar property.
createScalarXSD(String, String) - Static method in class chemaxon.marvin.io.MPropHandler
Creates a scalar property from the XSD type.
createSearcher(Transformer, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Constructs a searcher with the specified parameters.
createSearcherWithoutAromatization() - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that does not handle aromatization.
createSearcherWithoutAromatization(MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher that doesn't consider aromatization.
createSearcherWithoutAromatization(SimpleSearcher, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
Creates a searcher with the specified search options, other parameters (query, target, etc.) are copied from the specified searcher if possible (in case of BaseMolSearch).
createSelectionPanel(int) - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
createSelectionPanelAndProgressBar() - Method in class chemaxon.marvin.space.MSpaceEasy
Adds the basic MarvinSpace selection panel to the container.
createSetColoringParameter(Properties, MDocument) - Static method in class chemaxon.util.ImageExportUtil
 
createSgroupIterator() - Method in class chemaxon.util.iterator.IteratorFactory
Constructs an s-group iterator for the specified molecule of the factory.
createSmolecule() - Method in class chemaxon.struc.MoleculeGraph
Creates a Smolecule represenation of this molecule.
createSpacePanel(Molecule[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Creates space panel with given molecules, creates colored surface to each molecule.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Deprecated. 
createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
createStandardizedMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
Creates standardized molecule, the original input molecule is cloned.
createStrictNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a SubProgressObserver which ignores observed data.
createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates a sub-panel with a title.
createTopLeftConstraints() - Static method in class chemaxon.marvin.util.SwingUtil
Creates GridBagConstraints for the top left component.
createViewPanel(Molecule[]) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Creates view panel with given molecules, places molecule properties in formatted texts.
createViewPanel(Molecule[], int, int, int, int) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Creates view panel with given molecules, places molecule properties in formatted texts.
createVisitor(ImmutableList.Builder<T>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter
Constructs the specified visitor implementation.
createVisitor(ImmutableList.Builder<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter
Constructs the specified visitor implementation.
createWorkUnit() - Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
Creates a CompositeWorkUnit object composed of work units created by the factories.
createWorkUnit() - Method in interface chemaxon.util.concurrent.WorkUnitFactory
 
createWriter(OutputStream) - Method in class chemaxon.marvin.io.image.ImageExporter
Creator - Annotation Type in com.chemaxon.apidiscovery.annotations
Creator methods produce instances of specific classes.
CreatorWrapper<T> - Class in com.chemaxon.apidiscovery
CreatorWrapper acts as a type- and instance -dependent service loader.
CRITICAL_ERROR_MSG - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
Critical error message.
cross(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
Calculates the cross product of the two vectors
CrossedDoubleBondChecker - Class in chemaxon.checkers
A descendant of BondChecker for the detection of unspecified double bonds represented by crossed bond type.
CrossedDoubleBondChecker() - Constructor for class chemaxon.checkers.CrossedDoubleBondChecker
Default constructor
CrossedDoubleBondFixer - Class in chemaxon.fixers
CrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.CrossedDoubleBondFixer
Deprecated.
 
Cs - Static variable in class chemaxon.core.ChemConst
 
CSMDL_IN - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
CSMOL_OUT - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Compressed Molfiles and Rgfiles.
CSRDF - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Compressed RDfiles.
CSRXN_OUT - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Compressed Rxnfiles.
CSSDF_OUT - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Compressed SDfiles.
CSV - Static variable in class chemaxon.formats.MFileFormat
 
ctab - Variable in class chemaxon.struc.MoleculeGraph
Connection table.
CTransform3D - Class in chemaxon.struc
3D transformation matrix.
CTransform3D(CTransform3D) - Constructor for class chemaxon.struc.CTransform3D
Copy constructor.
CTransform3D() - Constructor for class chemaxon.struc.CTransform3D
Constructs an identity transformation.
CTSPECIFIC_H - Static variable in class chemaxon.struc.MolAtom
Deprecated.
As of Marvin 5.11
Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.
CTUMASK - Static variable in interface chemaxon.struc.StereoConstants
Double bond stereo mask.
CTUNKNOWN - Static variable in interface chemaxon.struc.StereoConstants
Deprecated.
As of Marvin 6.1,
Usage:
 In the specified methods the CIS|TRANS or
 CIS|TRANS|CTUNSPEC values are used instead.
 
CTUNSPEC - Static variable in interface chemaxon.struc.StereoConstants
Unspecified double bond.
Cu - Static variable in class chemaxon.core.ChemConst
 
CubeRecognizer - Class in chemaxon.formats.recognizer
Deprecated.
as of Marvin 2014.07.21.0 intended for internal use only
CubeRecognizer() - Constructor for class chemaxon.formats.recognizer.CubeRecognizer
Deprecated.
 
currentBond - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
Current bond pointer of the iterator.
cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox
Move the cursor down.
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
CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "customizationEnabled".
CustomMatcher - Interface in com.chemaxon.search
Interface for custom matching of atoms and bonds during search.
CustomMatcherFactory - Interface in com.chemaxon.search
Factory interface for creating CustomMatcher objects.
customMatcherFactory - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
customMatching(CustomMatcherFactory) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets the factory that is used to create a custom matcher.
customMatching(CustomMatcherFactory) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
customPaletteColors - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
CXSMARTS - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Extended SMARTS.
CXSMILES - Static variable in class chemaxon.formats.MFileFormat
ChemAxon Extended SMILES.
cyclomaticNumber() - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the smallest number of graph edges which must be removed such that no circuit remains.

D

D2S - Static variable in class chemaxon.formats.MFileFormat
Any document format recognized by Document to Structure (doc, odt, ...).
DataSgroup - Class in chemaxon.struc.sgroup
Data Sgroup.
DataSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.DataSgroup
Creates a Data S-group with the specified parent.
DataSgroup(DataSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.DataSgroup
Copy constructor.
DataSgroup(DataSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.DataSgroup
Copy constructor.
DAYLIGHT_DOWNWEDGE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Daylight style down wedge orientation flag.
DAYLIGHT_DOWNWEDGE_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Daylight style down wedge orientation.
Db - Static variable in class chemaxon.core.ChemConst
 
DBS_ALL - Static variable in interface chemaxon.struc.StereoConstants
Double bond stereo checking for all double bonds.
DBS_MARKED - Static variable in interface chemaxon.struc.StereoConstants
Double bond stereo checking for marked double bonds only.
DBS_NONE - Static variable in interface chemaxon.struc.StereoConstants
No double bond stereo checking.
deactivateActiveCell() - Method in class chemaxon.marvin.space.GraphicScene
Sets the active cell to be no longer active.
DEAROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
General dearomatization.
DEAROM_HUCKELCHECK - Static variable in class chemaxon.struc.MoleculeGraph
Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
DEAROM_HUCKELCHECK_EX - Static variable in class chemaxon.struc.MoleculeGraph
Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
dearomatize() - Method in class chemaxon.struc.Molecule
Dearomatize molecule.
dearomatize() - Method in class chemaxon.struc.MoleculeGraph
Dearomatize molecule.
dearomatize(int) - Method in class chemaxon.struc.MoleculeGraph
Dearomatize molecule.
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_TO_EA - Static variable in class chemaxon.calculations.dipole.DipoleResult
Debye to eA conversion upon multiplication.
decode(String, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
Reads attributes of the next section from a string.
decodeHIsotopeMass(int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
Extract H isotope information from the given Chemaxon compressed mol format code of the atom.
DECOMPRESS - Static variable in class chemaxon.formats.MdlCompressor
Decompression.
decorateSubPanel(JPanel, String) - Static method in class chemaxon.marvin.util.SwingUtil
Creates border and title for a panel.
decQProp(String) - Method in class chemaxon.struc.MolAtom
Decrements the value of a query property.
DECREASE_LINEAR - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will decrease when getting farther from the atom center.
DECREASE_RECIPROCAL_SQUARE - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will decrease when getting farther from the atom center.
DECREASE_SQUARE - Static variable in class chemaxon.marvin.space.SurfaceColoring
The property values will decrease when getting farther from the atom center.
decValenceProp() - Method in class chemaxon.struc.MolAtom
Decrements the value of the valence property.
DEF_MAXIONS - Static variable in class chemaxon.marvin.calculations.pKaPlugin
The default value of the number of ionizable atoms to consider.
DEF_TEMPERATURE - Static variable in class chemaxon.marvin.calculations.pKaPlugin
The default temperature in Kelvins.
DEFAULT - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
default factory id
DEFAULT - Static variable in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
 
DEFAULT - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default attributes object.
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_BALL_RADIUS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_BOND_DISTANCE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_BOND_RADIUS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_BOND_WIDTH - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_CACHE_SIZE - Static variable in class com.chemaxon.mapper.AutoMapper
default cache size
DEFAULT_CACHE_SIZE_PROPERTY - Static variable in class com.chemaxon.mapper.AutoMapper
cache size property key
DEFAULT_CHECKERS_CONFIG_PATH - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
path to default checker configuration list
DEFAULT_COLOR - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_COLOR - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
DEFAULT_CONFIG_FILE - Static variable in class chemaxon.marvin.plugin.PluginFactory
The default config file name.
DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
ChemAxon's default checker configuration path
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
The default location of ChemAxon standard checker runner configuration
DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.StructureCheckerFactory
Deprecated.
ChemAxon's default checker configuration file schema path
DEFAULT_DISSIMILARITY_THRESHOLD - Static variable in interface chemaxon.sss.SearchConstants
Default threshold value for similarity search.
DEFAULT_EQUILIBRIUM_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
Default equilibrium head width.
DEFAULT_H_BALL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_BOND_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_JOINT_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_SPACEFILL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_H_STICK_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_ISOVALUE - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
DEFAULT_L_BALL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_BOND_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_JOINT_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_SPACEFILL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_L_STICK_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_LINE_WIDTH - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_BALL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_BOND_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_JOINT_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_SPACEFILL_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_M_STICK_SLICE_PRECISION - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_MAX_CONSIDERED_RING_SIZE - Static variable in class com.chemaxon.search.mcs.McsSearchOptions
DEFAULT_MAX_CROSS_SIZE - Static variable in class chemaxon.struc.graphics.MPolyline
Default maximum cross size.
DEFAULT_NEAR_EDGE - Static variable in class chemaxon.marvin.space.GraphicCell
 
DEFAULT_OPTIONS - Static variable in interface chemaxon.struc.sgroup.Expandable
Default expansion/contraction options.
DEFAULT_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
the default priority value
DEFAULT_PROBE_RADIUS - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
DEFAULT_RADIUS - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
DEFAULT_RANDOM_SEED - Static variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
Default random seed.
DEFAULT_RECURSION_LEVEL - Static variable in class chemaxon.sss.screen.HashCode
 
DEFAULT_RESOLUTION - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
 
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_SAMPLING_ACCURACY - Static variable in class chemaxon.marvin.alignment.AtropIsomerDetector
DEFAULT_SAVE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "defaultSaveFormat".
DEFAULT_SEARCHTYPE - Static variable in interface chemaxon.sss.SearchConstants
Default search type equals SUBSTRUCTURE.
DEFAULT_SERVICE_CONFIGURATION_PATH - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
Path to default services configuration xml
DEFAULT_SERVICE_DESCRIPTOR_EDITOR_PROVIDER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service descriptor editor provider class
DEFAULT_SERVICE_DESCRIPTOR_READER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service descriptor reader class
DEFAULT_SERVICE_DESCRIPTOR_WRITER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service descriptor writer class
DEFAULT_SERVICE_DIALOG_PROVIDER_CLASSNAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
the Marvin Default service dialog provider class
DEFAULT_SIZE - Static variable in class chemaxon.marvin.space.monitor.Control
 
DEFAULT_STICK_RADIUS - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DEFAULT_SUPERSCRIPT_DELTAY - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default value of the y shift attribute in superscripts
DEFAULT_SUPERSCRIPT_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default value of the font scale attribute in superscripts
DEFAULT_SUPERSCRIPT_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes
Default value of the superscript level attribute in superscripts
DEFAULT_TAG_NAME - Static variable in class chemaxon.jep.Evaluator
Default SDFile tag to store the evaluation result.
DEFAULT_THICKNESS - Static variable in class chemaxon.struc.graphics.MPolyline
Default line thickness.
DEFAULT_TIMEOUT_LIMIT - Static variable in class chemaxon.sss.search.SearchOptions
 
DEFAULT_TOOL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "defaultTool".
DEFAULT_UNGROUP - Static variable in class chemaxon.struc.Molecule
Do not ungroup and do not expand S-group's children.
DEFAULT_USER_CHECKER_FILENAME - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
Default user defined checker file name for fallback.
DEFAULT_USER_SERVICE_CONFIGURATION_FILENAME - Static variable in class chemaxon.marvin.services.ServiceDescriptorTools
name of default user service configuration file
DEFAULT_VALUE - Static variable in class chemaxon.core.util.BondTable
The default (null) value in the matrix.
defaultCategories() - Static method in class com.chemaxon.calculations.solubility.SolubilityCategories
Creates default categories.
DefaultExternalStructureCheckerResult - Class in chemaxon.checkers.result
This descendant of DefaultStructureCheckerResult also implements the ExternalStructureCheckerResult interface thus providing a default implementation base class for external structure checkers' results.
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon, int) - 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
DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
Constructor which initialize all the properties.
DefaultPluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent
Work unit performing plugin calculation and returning the cached results.
DefaultPluginWorkUnit(CalculatorPluginOutput, boolean) - Constructor for class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
Constructor.
DefaultSolubilityCategory - Enum in com.chemaxon.calculations.solubility
Default solubility categories.
DefaultStructureCheckerResult - Class in chemaxon.checkers.result
This class is the default implementation of StructureCheckerResult
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
Constructor which initialize all the properties.
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
Constructor which initialize all the properties.
dehydrogenize(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
Deprecated.
deleteAllUserComparators() - Method in class chemaxon.sss.search.SearchOptions
Deletes all comparator added by the user.
deleteChar() - Method in class chemaxon.struc.graphics.MTextBox
Removes the character under the cursor.
deleteCharBackward() - Method in class chemaxon.struc.graphics.MTextBox
Removes the character before the cursor (backspace).
deleteUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
Deletes a given user defined comparator if found.
DESCRIPTION - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
description of checker
DESCRIPTION - Static variable in class chemaxon.fixers.StructureFixerDescriptor
description of fixer
Description - Annotation Type in com.chemaxon.apidiscovery.annotations
The annotated element has a description contained in this annotation.
description() - Method in enum com.chemaxon.calculations.solubility.DefaultSolubilityCategory
 
description() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
 
description() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
Description.
DESCRIPTOR_URI - Static variable in class chemaxon.marvin.services.json.JsonServiceDescriptor
Property key for Service descriptor as String
desiredLength(int, int, int, int) - Static method in class chemaxon.struc.MolBond
Desired length of a bond between two atoms in Angstroms.
destroySketcher() - Method in class chemaxon.marvin.beans.MViewPane
Closes all detached sketcher windows.
DETACH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "detach".
DETACHABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "detachable".
detectRecordPositions(IntVector) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
Detects positions of records in the input stream.
detectRecordPositions(IntVector) - Method in interface chemaxon.marvin.io.MRecordReader
Detects positions of records in the input stream.
determinant() - Method in class chemaxon.struc.CTransform3D
Computes the determinant of the matrix.
determinant2D() - Method in class chemaxon.struc.CTransform3D
Computes the determinant of the 2D matrix.
determineArrowDistance(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
Project the point (x,y,z) to the line of the reaction arrow 'ar'.
determinePosition(DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox
 
determineType(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
Determines whether a point should be in a reactant, in a product or in an agent.
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.
diffuse - Static variable in class chemaxon.marvin.space.monitor.Control
 
DihedralControl - Class in chemaxon.marvin.space.monitor
This control is to change a dihedral angle that is torsion a GraphicComponent.
DihedralControl(DihedralMonitor) - Constructor for class chemaxon.marvin.space.monitor.DihedralControl
Creates a new instance of DihedralControl
DihedralMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring dihedral.
DihedralMonitor() - Constructor for class chemaxon.marvin.space.monitor.DihedralMonitor
Creates a new instance of DihedralMonitor
DihedralRotator - Class in chemaxon.marvin.alignment
Rotates a dihedral in a 3D molecule
DihedralRotator(Molecule) - Constructor for class chemaxon.marvin.alignment.DihedralRotator
creates a rotator object
DihedralScanListener - Interface in chemaxon.marvin.alignment.atrop
Callback to track dihedral scan steps.
DihedralScanResult - Class in chemaxon.marvin.alignment.atrop
Results of a dihedral scan.
DihedralScanResult(BondInfo) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanResult
Construct for a dihedral.
dihedralScanStep(BondInfo, DihedralScanStep, Molecule, Molecule) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
Called when a dihedral scan step is performed.
DihedralScanStep - Class in chemaxon.marvin.alignment.atrop
One step in a dihedral scan.
DihedralScanStep(double, double) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanStep
Construct.
DIM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Colors are dim if enabled.
DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph
Dimension bits in flags.
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, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult
Constructor.
DipoleResult(double, double, double, DipoleResult.Unit, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult
Constructor.
DipoleResult.Unit - Enum in chemaxon.calculations.dipole
Dipole moment units.
dirty - Variable in class chemaxon.sss.search.SearchOptions
This flag is set to true whenever any of the options change.
DISABLE_AMINOACID_BOND_COLORING - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Coloring of peptide bridges
DISABLE_SPECIAL_NODES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "disableSpecialNodes".
disableNewEmfGenerator() - Static method in class chemaxon.util.ImageExportUtil
Disables the new .NET based EMF generator.
discardedPath - Variable in class chemaxon.checkers.StructureCheckOptions
The path of the invalid/unfixable output structures
Discovery - Class in com.chemaxon.apidiscovery
Utility methods for parameter discovery.
display(GLAutoDrawable) - Method in class chemaxon.marvin.space.GraphicScene
Warning: this function should not be called directly, use refresh() or redraw() instead.
DISPLAY_BOND_ORDER - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DISPLAY_QUALITY - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
Deprecated since Marvin 6.4. No settings is used intead of this, only High Quality exists from now on.
displayBondOrder - Variable in class chemaxon.marvin.space.MoleculeComponent
 
displayChanged(GLAutoDrawable, boolean, boolean) - Method in class chemaxon.marvin.space.GraphicScene
Called by the system.
displayChargeInCircle() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Display charge symbols in a circle.
displayInMarvinSpace - Variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
Display in MarvinSpace is enabled or not.
DispOptConsts - Interface in chemaxon.marvin.paint
Display option masks and offsets.
dispose(GLAutoDrawable) - Method in class chemaxon.marvin.space.GraphicScene
 
DISSIMILARITY_PROPERTY_NAME - Static variable in interface chemaxon.sss.SearchConstants
Name of the mrv/sdf property which stores the dissimilarity values.
distance(MolAtom, MolAtom) - Static method in class chemaxon.checkers.StructureCheckerHelper
Calculates the distance of two atoms.
distance(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculates the distance between two points.
distance2D(DPoint3) - Method in class chemaxon.struc.DPoint3
Calculates the distance between two points in the XY plane.
DISTANCE_CONSTANT - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the distance measured from the atom center extended by a constant value.
DISTANCE_FROM_VDW - Static variable in class chemaxon.marvin.space.SurfaceColoring
In case of distance weighted property mapping is the distance measured from the atom center extended by the van der Waals radius.
DISTANCE_FROM_VDW_EXTENDED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Is the distance measured from the atom center extended by the van der Waals radius plus a constant, typically the probe radius.
DISTANCE_WEIGHTED - Static variable in class chemaxon.marvin.space.SurfaceColoring
Will all affecting properties be mapped onto the surface weighted by atom distances.
DistanceBasedMetalloceneFixer - Class in chemaxon.fixers
A descendant of AbstractStructureFixer which converts incorrectly drawn metallocenes into multicenter based coordinate bond representation.
DistanceBasedMetalloceneFixer() - Constructor for class chemaxon.fixers.DistanceBasedMetalloceneFixer
 
distanceCount(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
Counts the given value in a row of the distance matrix.
distanceDegree(int) - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
Gets the 2D distance from the specified point.
distanceFrom(MoleculeGraph, double, double, CTransform3D) - Static method in class chemaxon.struc.graphics.MChemicalStruct
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlow
 
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
Gets the 2D distance from the specified point.
distanceFrom(double, double) - Method in class chemaxon.struc.MObject
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MObject
Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MPoint
Gets the 2D distance from the specified point.
DistanceMonitor - Class in chemaxon.marvin.space.monitor
Monitor for measuring distance between 2 components.
DistanceMonitor() - Constructor for class chemaxon.marvin.space.monitor.DistanceMonitor
Creates a new instance of DistanceMonitor
distanceRangeStore() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
 
DNA - Static variable in class chemaxon.formats.MFileFormat
DNA sequence.
DOC_AUTHOR - Static variable in class chemaxon.naming.DocumentToStructure
 
DOC_CREATION_DATE - Static variable in class chemaxon.naming.DocumentToStructure
 
DOC_LAST_AUTHOR - Static variable in class chemaxon.naming.DocumentToStructure
 
DOC_PATENT_ASSIGNEES - Static variable in class chemaxon.naming.DocumentToStructure
The assignees of the patent, separated by newline characters.
DOC_PATENT_ID - Static variable in class chemaxon.naming.DocumentToStructure
 
DOC_PATENT_INVENTORS - Static variable in class chemaxon.naming.DocumentToStructure
The inventors of the patent, separated by newline characters.
DOC_PATENT_IPC - Static variable in class chemaxon.naming.DocumentToStructure
The IPC classification(s) for the patent, separated by newline characters.
DOC_PATENT_IPCR - Static variable in class chemaxon.naming.DocumentToStructure
The IPCR classification(s) for the patent, separated by newline characters.
DOC_TITLE - Static variable in class chemaxon.naming.DocumentToStructure
 
doColoring() - Method in class chemaxon.marvin.space.SurfaceColoring
This function has to be called after proper parametrization of the SurfaceColoring object in case of custom properties.
doColoring(int) - Method in class chemaxon.marvin.space.SurfaceColoring
This function has to be called after proper parametrization of the SurfaceColoring object in case of built-in properties.
docProduced(MDocStorage, MDocument, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
Document retrieved from source.
DOCUMENT - Static variable in class chemaxon.naming.DocumentToStructure
The file name of the source document.
DOCUMENT_ANNOTATOR - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Document Annotator
DOCUMENT_METADATA - Static variable in class chemaxon.naming.DocumentToStructure
 
DOCUMENT_TO_DATABASE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Document to Structure
DOCUMENT_TO_STRUCTURE - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Document to Database
DocumentAnnotator - Class in chemaxon.naming.document.annotate
Generate a chemically annotated HTML view of a document.
DocumentAnnotator(File) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given document file.
DocumentAnnotator(InputStream) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator(InputStream, DocumentAnnotator.DocumentType) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
Constructs a DocumentAnnotator to annotate the given document.
DocumentAnnotator.DocumentType - Enum in chemaxon.naming.document.annotate
 
DocumentAnnotator.Listener - Interface in chemaxon.naming.document.annotate
 
DocumentAnnotator.ProgressInfo - Class in chemaxon.naming.document.annotate
 
DocumentAnnotatorOptions - Class in chemaxon.naming.document.annotate
 
DocumentAnnotatorOptions.Builder - Class in chemaxon.naming.document.annotate
 
DocumentAnnotatorOptions.ImageFormat - Enum in chemaxon.naming.document.annotate
 
DocumentExtractor - Class in chemaxon.naming
Deprecated.
use chemaxon.formats.MolImporter or chemaxon.naming.DocumentToStructure instead.
DocumentExtractor() - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
Creates a new document extractor.
DocumentExtractor(File) - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
If the file name ends with ".gz", the content will be uncompressed automatically.
DocumentExtractor(File, String) - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
If the file name ends with ".gz", the content will be uncompressed automatically.
DocumentExtractor(URL) - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
 
DocumentExtractor(URLConnection) - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
Create a document extractor for the given URL connection.
DocumentExtractor(Reader) - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
 
DocumentExtractor(String) - Constructor for class chemaxon.naming.DocumentExtractor
Deprecated.
Extract structures from a String.
DocumentExtractor.Hit - Class in chemaxon.naming
Deprecated.
An occurrence of a chemical name in the processed document.
DocumentExtractor.ProgressInfo - Class in chemaxon.naming
Deprecated.
 
DocumentExtractor.ProgressListener - Interface in chemaxon.naming
Deprecated.
 
DocumentStyleAPI - Class in chemaxon.marvin.sketch.swing.modules.documentstyle
API for DocumentStyle management.
DocumentStyleAPI() - Constructor for class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI
 
DocumentToStructure - Class in chemaxon.naming
 
DocumentToStructure() - Constructor for class chemaxon.naming.DocumentToStructure
 
done() - Method in interface com.chemaxon.calculations.common.SubProgressObserver
Notifies that the represented task is finished and no further work will be done.
DONOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
Donor sign displayed in GUI.
DONOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
DONR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
 
doPaste() - Method in class chemaxon.marvin.beans.MarvinPane
Invokes Paste actions.
doPaste() - Method in class chemaxon.marvin.beans.MSketchPane
Invokes Paste action.
doPaste() - Method in class chemaxon.marvin.beans.MViewPane
Invokes Paste action.
doSetSetSeqs(Molecule[], int, String) - Method in class chemaxon.marvin.view.MDocStorage
 
dotDisconnectedFormula() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the dot-disconnected molecular formula of a multifragment molecule.
dotDisconnectedIsotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the dot-disconnected isotope formula of a multifragment molecule.
dotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the dot-disconnected isotope formula of a multifragment molecule.
DotfileUtil - Class in chemaxon.util
Utility class for configuration file handling.
DotfileUtil() - Constructor for class chemaxon.util.DotfileUtil
 
DOTTED_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
DOUBLE_BOND - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
Deprecated.
 
DOUBLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond
Double or aromatic query bond type.
doubleStringWidth(String, MFont, FontMetrics, Graphics) - Method in class chemaxon.struc.graphics.MTextDocument.Section
Gets the width of a string as a floating point number.
doubleValue() - Method in class chemaxon.struc.prop.MDoubleProp
Gets the double floating point value.
DOWN - Static variable in class chemaxon.struc.MolBond
Single bond down flag.
DOWN_WEDGE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "downWedge".
DOWNWEDGE_MODES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Wedge bond display conventions.
DOWNWEDGE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
Down wedge orientation offset in display option flags.
DPoint3 - Class in chemaxon.struc
Point in three dimensional space.
DPoint3() - Constructor for class chemaxon.struc.DPoint3
Construct a zero point.
DPoint3(DPoint3) - Constructor for class chemaxon.struc.DPoint3
Copy constructor.
DPoint3(double, double, double) - Constructor for class chemaxon.struc.DPoint3
Construct a point from the specified coordinates.
DRAGGABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "draggable".
draw(GL2) - Method in class chemaxon.marvin.space.BoundingBox
Draws the box with the given GL2 in line mode.
draw() - Method in class chemaxon.marvin.space.GraphicCell
Makes the vieport draw this cell.
draw() - Method in class chemaxon.marvin.space.GraphicComponent
Draws the coordinate system of the component.
draw() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the MacroMolecule as letting its visualizers draw its parts.
draw() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
draw() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Draws the molecular surface, and recomputes it if the coordinates of the molecule have been changed.
draw() - Method in class chemaxon.marvin.space.MoleculeComponent
Called by GraphicCell from the Jogl rendering thread and draws the molecule.
draw() - Method in class chemaxon.marvin.space.monitor.AngleMonitor
Draws the anglemonitor as lines between the components, and an arc between the lines.
draw() - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
Draws dotted lines between the components, and a circle around the middle line.
draw() - Method in class chemaxon.marvin.space.monitor.DistanceMonitor
Draws solid line between the measured elements.
draw() - Method in class chemaxon.marvin.space.monitor.Label
Does nothing, because a label is drawn in plane or as a transparent component.
draw() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Draws nothing.
draw() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Draws the component if it is opaque.
draw() - Method in class chemaxon.marvin.space.PharmacophorePoint
Draws the entire component if it is opaque.
draw() - Method in class chemaxon.marvin.space.SurfaceComponent
Draws the surface if drawtype was DOTTED_TYPE or FILLED_TYPE.
draw2D - Variable in class chemaxon.marvin.space.monitor.Label
 
draw2DPart() - Method in class chemaxon.marvin.space.GraphicComponent
A component which draws (partly) in plane should overwrite this method.
draw2DPart() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the 2D parts of its visualizers.
draw2DPart() - Method in class chemaxon.marvin.space.monitor.Label
Draws the label when it is set to be drawn in plane.
draw2DPart() - Method in class chemaxon.marvin.space.monitor.PositionMonitor
Draws the Control of the PositionMonitor.
DRAW_TYPE_BALL - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_BALL_AND_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_BALL_AND_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_SPACEFILL - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
DRAW_TYPES - Static variable in class chemaxon.marvin.space.PharmacophoreArrow
 
DRAW_TYPES - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
drawAtomSelection(int) - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
drawAtomSelection(int) - Method in class chemaxon.marvin.space.MoleculeComponent
To make selection faster we don't draw the atoms themself into the selection buffer, but we draw simple polygons instead.
drawBorders() - Method in class chemaxon.marvin.space.GraphicCell
Draw borders of the cell.
drawBoundingBox() - Method in class chemaxon.marvin.space.GraphicComponent
Vizualises the bounding box.
drawCell() - Method in class chemaxon.marvin.space.GraphicCell
Draws all components of the cell.
drawCoordinateAxes() - Method in class chemaxon.marvin.space.GraphicComponent
Draws the local coordinate axes, the origin is the transformation center
drawHydrogens - Variable in class chemaxon.marvin.space.MoleculeComponent
 
drawProperties - Variable in class chemaxon.marvin.space.GraphicComponent
Common drawing related properties that affect all three quality modes.
drawRawSurface() - Method in class chemaxon.marvin.space.SurfaceComponent
 
drawRelation - Variable in class chemaxon.marvin.space.monitor.Label
 
drawSelection(int) - Method in class chemaxon.marvin.space.GraphicComponent
Draws the component in the given mode (usually in selection mode), the rendering mode is for checking.
drawSelection(int) - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the component in the given mode (usually in selection mode).
drawSelection(int) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
 
drawSelection(int) - Method in class chemaxon.marvin.space.MoleculeComponent
 
drawSelection(int) - Method in class chemaxon.marvin.space.SurfaceComponent
 
drawSmoothBackground() - Method in class chemaxon.marvin.space.GraphicCell
 
drawSphere() - Method in class chemaxon.marvin.space.GraphicCell
Draws the rotation sphere.
drawSurface() - Method in class chemaxon.marvin.space.SurfaceComponent
 
drawTransparentPart() - Method in class chemaxon.marvin.space.GraphicComponent
A component having transparent parts should override this method, drawing the transparent parts here.
drawTransparentPart() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Draws the transparent parts of its visualizers.
drawTransparentPart() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
drawTransparentPart() - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
Draws the surface if it was transparent or mesh.
drawTransparentPart() - Method in class chemaxon.marvin.space.MoleculeComponent
Draws the molecule if the drawing type was wire.
drawTransparentPart() - Method in class chemaxon.marvin.space.monitor.Label
Renders the label in 3d as a transparent object.
drawTransparentPart() - Method in class chemaxon.marvin.space.PharmacophoreArrow
Draws transparent parts of the component if there is any.
drawTransparentPart() - Method in class chemaxon.marvin.space.PharmacophorePoint
Draws transparent parts of the component if there is any.
drawTransparentPart() - Method in class chemaxon.marvin.space.SurfaceComponent
Draws the surface if drawtype was MESH_TYPE or TRANSPARENT_TYPE.
drawType - Variable in class chemaxon.marvin.space.GraphicComponent
The actual drawing type of the component.
drawType - Variable in class chemaxon.marvin.space.MoleculeComponent
 
drawTypes - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
Ds - Static variable in class chemaxon.core.ChemConst
 
DT_FORMATTED - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: formatted.
DT_NUMERIC - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: numeric.
DT_TEXT - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: text.
DT_UNSPEC - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: unspecified.
DT_URL - Static variable in class chemaxon.struc.sgroup.DataSgroup
Field type: url.
DUPLICATE - Static variable in interface chemaxon.sss.SearchConstants
Duplicate search (formerly called perfect).
Dy - Static variable in class chemaxon.core.ChemConst
 
DynamicArgument<CT,RT> - Class in chemaxon.marvin.services
ServiceArguments implementing this interface should support automatic evaluation of arguments before service call based on context.
NOTE: subclasses MUST HAVE default constructor to use from Marvin Sketch
DynamicArgument() - Constructor for class chemaxon.marvin.services.DynamicArgument
 
DynamicArgument(String) - Constructor for class chemaxon.marvin.services.DynamicArgument
 
DYNAMICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin
pKa's prefix (acidic/basic) does depend on the submitted micro state

E

E_SINK - Static variable in class chemaxon.struc.graphics.MEFlow
Electron sink.
E_SOURCE - Static variable in class chemaxon.struc.graphics.MEFlow
Electron source.
eccentricity(int) - Method in class chemaxon.calculations.TopologyAnalyser
Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
ECFP_FCFP - Static variable in class chemaxon.license.LicenseManager
Identifier of product: Molecular Descriptors
EDITABLE - Static variable in class chemaxon.marvin.beans.MViewPane
Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinView in a new window.
EDITABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
Identifier of parameter: "editable".
EDITOR_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
editor class name property of checker
electronegOf(int) - Static method in class chemaxon.struc.MolAtom
Gets 10 times the electronegativity value for the specified element.
electronRadious - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
 
ELEMENT_COUNT - Static variable in class chemaxon.core.ChemConst
Number of elements in the periodic system
ELEMENT_COUNT - Static variable in class chemaxon.struc.MolAtom
Number of elements in the periodic system
ElementalAnalyser - Class in chemaxon.calculations
Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyser() - Constructor for class chemaxon.calculations.ElementalAnalyser
 
ElementalAnalyserPlugin - Class in chemaxon.marvin.calculations
Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.ElementalAnalyserPlugin
 
ElementalAnalysis - Interface in com.chemaxon.calculations.elemanal
Calculates molecular formula, mass, MS mass and composition.
elementList - Static variable in class chemaxon.marvin.space.MoleculeComponent
 
ELEMENTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "elements".
EMF - Static variable in class chemaxon.formats.MFileFormat
Windows Enhanced Metafiles.
EmfExporter - Class in chemaxon.marvin.io.formats.vectgraphics
Emf export with options.
EmfExporter(EmfExporter.Builder<?>) - Constructor for class chemaxon.marvin.io.formats.vectgraphics.EmfExporter
 
EmfExporter() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.EmfExporter
Creates a EmfExporter with default options.
EmfExporter.Builder<T extends EmfExporter.Builder<T>> - Class in chemaxon.marvin.io.formats.vectgraphics
 
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.sketch.SketchParameterConstants
Identifier of parameter: "2dviewerEnabled".
ENABLED_3D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "3dviewerEnabled".
enclosesPoint(double, double) - Method in class chemaxon.struc.graphics.MBracket
Checks if a specified point is enclosed by this bracket.
encode(MFont, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
Returns the string representation of the attributes.
encoding - Variable in class chemaxon.marvin.io.PositionedInputStream
The encoding.
END_CHARACTER - Static variable in class chemaxon.naming.DocumentToStructure
The ending character offset since the beginning of the document, for text formats (html, xml, txt).
endGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream
Ends grabbing lines.
endHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
Changes the hourglass cursor back to normal at the end of a long operation.
ENDO - Static variable in interface chemaxon.struc.StereoConstants
Non-CIP stereodescriptor, endo (relative configuration).
endRecord(boolean) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
It must be called at the end of record.
endReuse(int) - Method in class chemaxon.struc.Molecule
End reusing atoms.
endReuse(int) - Method in class chemaxon.struc.RgMolecule
End reusing atoms.
endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument
Tests whether the document ends with the specified character.
endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
Tests whether this text portion ends with the specified character.
EnhancedStereo - Class in com.chemaxon.calculations.stereoanal.stereocenters
Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.
EnhancedStereo(StereoConstants.EnhancedStereoType, int) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Creates enhanced stereo representation.
EnhancedStereo(StereoConstants.EnhancedStereoType) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
Creates enhanced stereo representation.
EnhancedStereoGroup - Class in com.chemaxon.calculations.stereoanal.stereocenters
Enhanced stereo descriptor class.
EnhancedStereoGroup(EnhancedStereo, List<TetrahedralStereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
Creates enhanced stereo group.
enqueueUpdate() - Method in class chemaxon.marvin.view.swing.TableSupport
Enqueues an update task.
EPS - Static variable in class chemaxon.formats.MFileFormat
Encapsulated PostScript vector image format.
EPSILON - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
 
EPSILON - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
The microspecies is ignored if its distribution is less than EPSILON for all pH values.
equals(Object) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
 
equals(Object) - Method in class chemaxon.checkers.AbstractStructureChecker
 
equals(Object) - Method in class chemaxon.checkers.AromaticityErrorChecker
 
equals(Object) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
 
equals(Object) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
 
equals(Object) - Method in class chemaxon.checkers.result.AromaticityCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.BondAngleCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.BondLengthCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
 
equals(Object) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.ReactionCheckerResult
Deprecated.
 
equals(Object) - Method in class chemaxon.checkers.result.RgroupCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.SgroupCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.result.SubstructureCheckerResult
 
equals(Object) - Method in class chemaxon.checkers.StructureCheckerDescriptor
 
equals(Object) - Method in class chemaxon.checkers.ValencePropertyChecker
 
equals(Object) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
 
equals(Object) - Method in class chemaxon.fixers.StructureFixerDescriptor
 
equals(Object) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
 
equals(Object) - Method in class chemaxon.marvin.space.ComponentElement
 
equals(Object) - Method in class chemaxon.sss.search.MarkushFeature
 
equals(Object) - Method in class chemaxon.sss.search.SearchHit
 
equals(Object) - Method in class chemaxon.struc.AtropStereoDescriptor
 
equals(Object) - Method in class chemaxon.struc.AxialStereoDescriptor
 
equals(Object) - Method in class chemaxon.struc.CisTransStereoDescriptor
 
equals(Object) - Method in class chemaxon.struc.CTransform3D
 
equals(CTransform3D, double) - Method in class chemaxon.struc.CTransform3D
 
equals(Object) - Method in class chemaxon.struc.DPoint3
Two points equal if their coordinates equal.
equals(Object) - Method in class chemaxon.struc.graphics.MAtomSetPoint
Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.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(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether two attributes objects equal or not.
equals(Object) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether two attributes objects equal or not.
equals(Object) - Method in class chemaxon.struc.MPoint
Two points equal if their location equals.
equals(Object) - Method in class chemaxon.struc.prop.MBooleanProp
 
equals(Object) - Method in class chemaxon.struc.prop.MCollectionProp
 
equals(Object) - Method in class chemaxon.struc.prop.MDoubleArrayProp
 
equals(Object) - Method in class chemaxon.struc.prop.MDoubleProp
 
equals(Object) - Method in class chemaxon.struc.prop.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.MObjectProp
 
equals(Object) - Method in class chemaxon.struc.prop.MStringProp
 
equals(Object) - Method in class chemaxon.struc.StereoActivePart
 
equals(Object) - Method in class chemaxon.struc.TetrahedralStereoDescriptor
 
equalsHead(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the head bonds equal the given bonds.
equalsNext(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
Tests whether the attributes of two neighboring sections equal or not.
equalsTail(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Decides whether the tail bonds equal the given bonds.
equalsTo(Object, int[]) - Method in class chemaxon.struc.AtropStereoDescriptor
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.AxialStereoDescriptor
 
equalsTo(Object, int[]) - Method in interface chemaxon.struc.CIPStereoDescriptorIface
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.CisTransStereoDescriptor
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.StereoActivePart
 
equalsTo(Object, int[]) - Method in class chemaxon.struc.TetrahedralStereoDescriptor
 
EQUILIBRIUM - Static variable in class chemaxon.struc.RxnMolecule
Resonance arrow, the same as the two-headed double reaction arrow.
Er - Static variable in class chemaxon.core.ChemConst
 
ErrorProcessor - Interface in chemaxon.util
Error processing interface.
ErrorReport - Class in com.chemaxon.calculations.stereoanal
Error reporting class.
ErrorReport(AtomSelection, String, Optional<? extends StereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport
Constructs new error report.
ErrorReport(AtomSelection, String) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport
Constructs new error report.
errors() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
Error reports.
errorType - Variable in class chemaxon.checkers.AbstractStructureChecker
The error type of the current checker.
Es - Static variable in class chemaxon.core.ChemConst
 
ESCAPE_CHAR - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "escapeChar".
estimateNumRecords() - Method in class chemaxon.formats.MolImporter
Estimates the total number of records.
estimateNumRecords() - Method in class chemaxon.marvin.io.ArrayMDocSource
Estimates the total number of records.
estimateNumRecords() - Method in class chemaxon.marvin.io.MDocSource
Estimates the total number of records.
estimateProgress() - Method in interface chemaxon.util.iterator.MoleculeIterator
Estimates the iteration progress.
Eu - Static variable in class chemaxon.core.ChemConst
 
evaluate(ChemContext) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression.
evaluate(CT) - Method in class chemaxon.marvin.services.DynamicArgument
Evaluates the dynamic argument based on context
evaluate_boolean(ChemContext) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result boolean.
evaluate_booleans(ChemContext) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result to boolean[].
evaluate_double(ChemContext) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result to double.
evaluate_doubles(ChemContext) - Method in class chemaxon.jep.ChemJEP
Evaluates the expression and converts the result to double[].
Evaluator - Class in chemaxon.jep
Evaluates Chemical Terms expressions.
Evaluator() - Constructor for class chemaxon.jep.Evaluator
Default constructor.
Evaluator(Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(String) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File, Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(File, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator
Deprecated. 
Evaluator(String, Standardizer) - Constructor for class chemaxon.jep.Evaluator
Constructor.
Evaluator(String, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator
Deprecated. 
EVALUATOR_DEFAULTS_FILE - Static variable in class chemaxon.jep.Evaluator
Default Function/Plugin settings filename.
EVALUATOR_NAMED_MOLS_FILE - Static variable in class chemaxon.jep.Evaluator
Default named molecule set filename.
EVALUATOR_SCRIPT_FILE - Static variable in class chemaxon.jep.Evaluator
Initial script filename.
EVEN - Static variable in class chemaxon.calculations.stereo.Stereochemistry
 
exactMass() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.
exactMass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
exactMassPrecision() - Method in class chemaxon.calculations.ElementalAnalyser
Calculates the precision of the monoisitopic weight (number of significant decimal digits).
exactQueryAtomMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
exactQueryAtomMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether generic query atoms should be matched only to atoms of exactly the same type.
exactQueryAtomMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
exactQueryBondMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
 
exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
Sets whether generic query bonds should be matched only to bonds of exactly the same type.
exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
 
EXCLUDED_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
 
exclusiveSelection(int) - Method in class chemaxon.marvin.space.GraphicCell
Exclusive selection in the given component.
exclusiveSelection() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
exclusiveSelection(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the the given part of the component to be selected, and sets every other parts not to be selected.
exclusiveSelection(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Exclusive selection in the given component in its container cell.
exclusiveSelection() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
exclusiveSelection() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the previously picked but unprocessed element to be selected, and sets every other parts not to be selected.
exit() - Method in class chemaxon.marvin.beans.MarvinPane
Closes all windows opened by this MarvinPane and saves user initialization file.
exit(int) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Terminate execution with given status code.
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.
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.
EXPLICIT_H - Static variable in class chemaxon.marvin.common.ParameterConstants
Deprecated.
since 5.3
ExplicitHydrogenChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting explicit hydrogens.
ExplicitHydrogenChecker() - Constructor for class chemaxon.checkers.ExplicitHydrogenChecker
Default constructor All types of explicit hydrogens will be searched.
ExplicitHydrogenChecker(Map<String, String>) - Constructor for class chemaxon.checkers.ExplicitHydrogenChecker
Parameterized constructor If map contains lonely/charged/mapped/isotopic/radical/wedged keys with value false then hydrogens with these types won't be detected.
ExplicitHydrogenFixer - Class in chemaxon.fixers
ExplicitHydrogenFixer() - Constructor for class chemaxon.fixers.ExplicitHydrogenFixer
Deprecated.
 
ExplicitHydrogenResult - Class in chemaxon.checkers.result
A descendant of DefaultStructureCheckerResult for identifying explicit hydrogen problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.
ExplicitHydrogenResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.ExplicitHydrogenResult
Constructor which initialize all the properties.
explicitHydrogens - Variable in class chemaxon.marvin.plugin.CalculatorPlugin
explicit hydrogens of the input molecule stored here key: index of the "parent" atom on the input molecule value: the hydrogen atom
ExplicitLonePairChecker - Class in chemaxon.checkers
A descendant of AtomChecker detecting lone pair type atoms.
ExplicitLonePairChecker() - Constructor for class chemaxon.checkers.ExplicitLonePairChecker
Default constructor
explicitLonePairs() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
Display the explicit lone pairs instead of the implicit lone pairs if lone pair displaying is switched on.
export(NMRSpectrum, double, double, double) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Returns the x-y point pairs of an NMR spectrum.
exportToBinFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter
Creates a binary representation of the document.
exportToBinFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Creates a binary representation of the molecule.
exportToBinFormat(String) - Method in class chemaxon.struc.MDocument
Deprecated.
As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String).
exportToBinFormat(String) - Method in class chemaxon.struc.Molecule
Deprecated.
exportToFormat(MDocument, String) - Static method in class chemaxon.formats.MolExporter
Creates a string representation of the document.
exportToFormat(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Creates a string representation of the molecule.
exportToFormat(String) - Method in class chemaxon.struc.MDocument
Deprecated.
As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String)
exportToFormat(String) - Method in class chemaxon.struc.Molecule
Deprecated.
As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
exportToJcampDX(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Exports the NMR spectrum into JCAMP-DX format.
exportToJcampDX(NMRSpectrum, int) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Exports the NMR spectrum into JCAMP-DX format.
exportToMol(NMRSpectrum) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Returns a molecule with its NMR spectrum property.
exportToMol(NMRSpectrum, String) - Static method in class chemaxon.calculations.nmr.io.NMRExporter
Returns a molecule with its NMR spectrum property.
exportToObject(MDocument, String) - Static method in class chemaxon.formats.MolExporter
Creates a String, byte[] array or Image representation of the document.
exportToObject(Molecule, String) - Static method in class chemaxon.formats.MolExporter
Creates a String, byte[] array or Image representation of the molecule.
exportToObject(Molecule[], String, MolExportModule) - Static method in class chemaxon.formats.MolExporter
Creates a String, byte[] array or Image representation of the given molecules.
exportToObject(String) - Method in class chemaxon.struc.MDocument
Deprecated.
As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String)
exportToObject(String) - Method in class chemaxon.struc.Molecule
Deprecated.
As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
extend(float) - Method in class chemaxon.marvin.space.BoundingBox
Makes the bounding box being larger or smaller by the given value in each direction.
extendSelection(int) - Method in class chemaxon.marvin.space.GraphicCell
Additive selection in the given component, so the previously picked part of the component will be selected, and all selection remains as is.
extendSelection() - Method in class chemaxon.marvin.space.GraphicComponent
Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
extendSelection(ComponentElement) - Method in class chemaxon.marvin.space.GraphicComponent
Sets the the given part of the component to be selected, and leaves other parts as they are.
extendSelection(UOID) - Method in class chemaxon.marvin.space.GraphicScene
Additive selection in the given component in its container cell.
extendSelection() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
extendSelection() - Method in class chemaxon.marvin.space.MoleculeComponent
Sets the previously picked but unprocessed element to be selected, and leaves other parts as they are.
ExternalStructureChecker - Class in chemaxon.checkers
ExternalStructureChecker class provides a super class for externally implemented structure checkers.
ExternalStructureChecker(String) - Constructor for class chemaxon.checkers.ExternalStructureChecker
This constructor creates an external structure checker instance with the given error code
ExternalStructureCheckerResult - Interface in chemaxon.checkers.result
This interface is an extension of StructureCheckerResult that supports external StructureChecker development.
EXTRA_BONDS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "extraBonds".
EXTRA_TEMPLATES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
Identifier of parameter: "xtmpls".
extraFlavor - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
 
EZ_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
E/Z visibility flag.
EZ_LABEL_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
Show E/Z.
EZ_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
Identifier of parameter: "ezVisible".
EZDoubleBondChecker - Class in chemaxon.checkers
A descendant of AbstractStructureChecker detecting double bonds, that can be cis or trans.
EZDoubleBondChecker() - Constructor for class chemaxon.checkers.EZDoubleBondChecker
Initializes the EZ double bond checker

F

F - Static variable in class chemaxon.core.ChemConst
 
F_ARCHIVE - Static variable in class chemaxon.formats.MFileFormat
General archive format that stores a file in another format.
F_BINARY - Static variable in class chemaxon.formats.MFileFormat
Import/export module handles binary (byte array) data.
F_COORDS - Static variable in class chemaxon.formats.MFileFormat
The format can store atom coordinates if this flag is set.
F_EXPORT - Static variable in class chemaxon.formats.MFileFormat
Export is possible if this flag is set.
F_GRAPHICS - Static variable in class chemaxon.formats.MFileFormat
File format readable by a graphics program (image viewer, ray tracer etc.).
F_IMAGE - Static variable in class chemaxon.formats.MFileFormat
2D image file format, readable by image viewers.
F_IMPORT - Static variable in class chemaxon.formats.MFileFormat
Import is possible if this flag is set.
F_MIXED - Static variable in class chemaxon.formats.MFileFormat
Storage of records in different formats is possible if this flag is set.
F_MOL_MISSING - Static variable in class chemaxon.marvin.io.MRecord
Molecule (or reaction) is missing from the record.
F_MOLECULE - Static variable in class chemaxon.formats.MFileFormat
The format can store molecule(s) if this flag is set.
F_MULTIPLE_RECORDS_LEGAL - Static variable in class chemaxon.formats.MFileFormat
The format is designed to store multiple records if this flag is set.
F_MULTIPLE_RECORDS_POSSIBLE - Static variable in class chemaxon.formats.MFileFormat
The import/export modules can handle files with multiple records if this flag is set, but according to the format definition it is not legal.
F_OBJECT - Static variable in class chemaxon.formats.MFileFormat
Import/export module creates or reads a java object.
F_REACTION - Static variable in class chemaxon.formats.MFileFormat
The format can store reaction(s) if this flag is set.
F_RECOGNIZER - Static variable in class chemaxon.formats.MFileFormat
Format recognizer exists if this flag is set.
F_SINGLE_LINE - Static variable in class chemaxon.formats.MFileFormat
Format uses one line per structure.
F_USER_DEFINED - Static variable in class chemaxon.formats.MFileFormat
User defined format.
F_XML - Static variable in class chemaxon.formats.MFileFormat
The format is XML based if this flag is set.
Factory() - Constructor for class chemaxon.marvin.alignment.MCSAlignment.Factory
 
fadeSelected() - Method in class chemaxon.marvin.space.GraphicComponent
A descendant should overwrite this method to have its selection became faded.
fadeSelected() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The selected visualizers will be hidden.
fadeSelected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
fadeSelected() - Method in class chemaxon.marvin.space.MoleculeComponent
The selected atoms will be faded.
fadeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all selected components to faded.
fadeSelectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Sets the drawing mode of all selected elements to faded so it will be hardly visible, and prevents them from clicking.
fadeUnselected() - Method in class chemaxon.marvin.space.GraphicComponent
A descendant should overwrite this method to have all but its selection became faded.
fadeUnselected() - Method in class chemaxon.marvin.space.MacroMoleculeComponent
The unselected visualizers will be hidden.
fadeUnselected() - Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
 
fadeUnselected() - Method in class chemaxon.marvin.space.MoleculeComponent
The unselected atoms will be faded.
fadeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicCell
Sets all selected components to faded.
fadeUnselectedComponents() - Method in class chemaxon.marvin.space.GraphicScene
Sets the drawing mode of all unselected elements to faded so it will be hardly visible, and prevents them from clicking.
FALSE - Static variable in class chemaxon.jep.ChemJEP
Logical result value: FALSE.
FAST_COORDS - Static variable in interface chemaxon.struc.sgroup.Expandable
Fast coordinate calculation in expand.
FASTA - Static variable in class chemaxon.formats.MFileFormat
FASTA file format
FASTA_DNA - Static variable in class chemaxon.formats.MFileFormat
FASTA file format with DNA sequence
FASTA_PEPTIDE - Static variable in class chemaxon.formats.MFileFormat
FASTA file format with peptide sequence
FASTA_RNA - Static variable in class chemaxon.formats.MFileFormat
FASTA file format with RNA sequence
FastUpperBoundCalculator - Class in com.chemaxon.search.mcs.upperbound
This class implements a simple upper bound calculator for the MCS problem.
FastUpperBoundCalculator() - Constructor for class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator
 
Fe - Static variable in class chemaxon.core.ChemConst
 
fileEndPosition - Variable in class chemaxon.marvin.io.MRecord
 
files - Variable in class chemaxon.checkers.StructureCheckOptions
List of the input files
fileStartPosition - Variable in class chemaxon.marvin.io.MRecord
 
FILLED_TYPE - Static variable in class chemaxon.marvin.space.SurfaceComponent
 
fillInStackTrace() - Method in exception chemaxon.naming.NameFormatException
 
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.Molecule
Adds all atoms and bonds to the specified molecule.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RgMolecule
Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
fillSelectionMolecule(SelectionMolecule) - Method in class chemaxon.struc.RxnMolecule
Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
fillWithNulls() - Method in class chemaxon.marvin.view.MDocStorage
Set all stored document entries to null.
filter(List<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
Filter stereo centers.
FILTER_DIM0 - Static variable in class chemaxon.formats.MolExporter
Molecule filter for cleaning 0D molecules only.
FILTER_ONE_ATTACHMENT - Static variable in class chemaxon.marvin.util.MolFragLoader
Filter object for accepting fragments with one attachment point.
FILTER_TWO_ATTACHMENTS - Static variable in class chemaxon.marvin.util.MolFragLoader
Filter object for accepting fragments with two attachment points.
FILTER_VALENCE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
Filter constant: valence filter.
FilteredCase(String) - Constructor for exception chemaxon.naming.NameFormatException.FilteredCase
 
FilteredCase(String, Throwable) - Constructor for exception chemaxon.naming.NameFormatException.FilteredCase
 
finalize() - Method in class chemaxon.formats.MolExporter
 
finalize() - Method in class chemaxon.marvin.space.BoundingBox
 
finalize() - Method in class chemaxon.marvin.space.monitor.DihedralControl
 
finalize() - Method in class chemaxon.marvin.space.SurfaceColoring
 
find() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
Performs MCS search according to the specified options.
findAll() - Method in class chemaxon.sss.search.Search
Looks for all matching patterns in the molecule.
findAllGroups() - Method in class chemaxon.sss.search.Search
Returns the group hits corresponding to all hits.
findAllHits() - Method in class chemaxon.sss.search.Search
Looks for all matching patterns in the molecule.
findAllSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule
Finds all smallest S-groups containing the specified atom.
findAtom(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Finds an atom in the atoms array.
findAtomClone(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
Finds the clone of an atom.
findAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem
Returns the atomic number of the element in the periodic system specified by its symbol.
findAttachAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Gets the attachment atom of attachment point with the smallest order.
findBasicFrags(Class<C>) - Method in class chemaxon.struc.MoleculeGraph
Determines the disconnected fragments and puts them into an array.
findBond(MolBond) - Method in class chemaxon.struc.MoleculeGraph
Finds a bond in the bonds array.
findComponentIds() - Method in class chemaxon.struc.MoleculeGraph
Deprecated.
As of Marvin 6.0, replaced by MoleculeGraph.getFragIds(int) and MoleculeGraph.FRAG_BASIC.
Usage:
mol.getFragIds(MoleculeGraph.FRAG_BASIC);
findComponentIds(int[]) - Method in class chemaxon.struc.MoleculeGraph
Assigns a component ID to each connected component formed by the specified atom indexes.
findContainingMulticenterSgroup(MolAtom) - Method in class chemaxon.struc.Molecule
Gets the containing multicenter S-group of a multicenter atom.
findContractableSgroup() - Method in class chemaxon.struc.Molecule
Finds an expanded residue.
findCrossingBonds() - Method in class chemaxon.struc.Sgroup
Finds the crossing bonds.
findCrossingBonds() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
Finds the crossing bonds.
findCrossingBonds() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
Finds the crossing bonds.
findExpandableSgroup() - Method in class chemaxon.struc.Molecule
Finds a contracted residue.
findFirst() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
Overlays the molecule to align on the reference using the predefined atom pairs.
findFirst() - Method in class chemaxon.sss.search.Search
Looks for the first matching pattern in the target molecule.
findFirstGroup() - Method in class chemaxon.sss.search.Search
Returns the group hit corresponding to the first hit.
findFirstHit() - Method in class chemaxon.sss.search.Search
Looks for the first matching pattern in the target molecule.
findFormats(String, long, long) - Static method in class chemaxon.formats.MFileFormatUtil
Gets a list of formats.
findFrag(int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph