Index (Marvin API documentation (c) 1998-2005 ChemAxon Ltd.)

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A

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.
ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin: Acceptor sign displayed in GUI.
ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin: Constant denoting acidic pKa.
AGENTS - Static variable in class chemaxon.struc.RxnMolecule: "Agent" structure type.
ALIPHATIC - Static variable in class chemaxon.struc.MolAtom: Aliphatic query atom.
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.
AROMATIC - Static variable in class chemaxon.struc.MolAtom: Aromatic query atom.
AROMATIC - Static variable in class chemaxon.struc.MolBond: Aromatic bond type.
AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom: Aromatic or aliphatic query atom.
AROM_CHEMAXON - Static variable in class chemaxon.struc.MoleculeGraph: Chemaxon aromatization.
AROM_DAYLIGHT - Static variable in class chemaxon.struc.MoleculeGraph: Daylight aromatization (modified Huckel rule).
ARROW - Static variable in class chemaxon.struc.MolBond: Reaction arrow.
ARROW_BACK_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline: Arrow points back.
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.
ATOM - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Calculation domain type: calculation refers to atoms.
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.
ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom: Number of atom types in the elements array
ATTACH1 - Static variable in class chemaxon.struc.MolAtom: Attachment point on first site.
ATTACH2 - Static variable in class chemaxon.struc.MolAtom: Attachment point on second site.
ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom: Attachment point on first and second site.
ArrowSM - class chemaxon.marvin.sketch.modules.ArrowSM.: Arrow drawing mode.
ArrowSM() - Constructor for class chemaxon.marvin.sketch.modules.ArrowSM: Creates a line sketch mode object.
ArrowSM(ArrowSM) - Constructor for class chemaxon.marvin.sketch.modules.ArrowSM: Copy constructor.
ArrowSM.Regular - class chemaxon.marvin.sketch.modules.ArrowSM.Regular.
ArrowSM.Regular() - Constructor for class chemaxon.marvin.sketch.modules.ArrowSM.Regular
ArrowSM.Regular(ArrowSM.Regular) - Constructor for class chemaxon.marvin.sketch.modules.ArrowSM.Regular
ArrowSM.TwoHeaded - class chemaxon.marvin.sketch.modules.ArrowSM.TwoHeaded.
ArrowSM.TwoHeaded() - Constructor for class chemaxon.marvin.sketch.modules.ArrowSM.TwoHeaded
ArrowSM.TwoHeaded(ArrowSM.TwoHeaded) - Constructor for class chemaxon.marvin.sketch.modules.ArrowSM.TwoHeaded
AtomSM - class chemaxon.marvin.sketch.AtomSM.: Atom placement mode.
AtomSM(MolEditor, MolAtom) - Constructor for class chemaxon.marvin.sketch.AtomSM: Creates a sketcher atom object for the specified molecule editor.
AutoMapper - class chemaxon.marvin.modules.AutoMapper.: AutoMapper finds the best mapping from reactant side atoms to product side atoms of a reaction.
AutoMapper() - Constructor for class chemaxon.marvin.modules.AutoMapper: Creates a new instance of AutoMapper.
add(CNode) - Method in class chemaxon.struc.CGraph: Adds a node to the graph.
add(CEdge) - Method in class chemaxon.struc.CGraph: Adds an edge to the graph.
add(CEdge) - Method in class chemaxon.struc.CNode: Add an edge if it had not been already added.
add(CEdge) - Method in class chemaxon.struc.MolAtom: Add an edge if it had not been already added.
add(CNode) - Method in class chemaxon.struc.RgMolecule: Adds an atom to the root structure.
add(CEdge) - Method in class chemaxon.struc.RgMolecule: Adds a bond to the root structure.
add(CNode) - Method in class chemaxon.struc.RxnMolecule: Adds an atom to a reactant, product or agent structure.
add(CEdge) - Method in class chemaxon.struc.RxnMolecule: Adds a bond to a reactant, product, agent.
add(CEdge) - Method in class chemaxon.struc.SelectionMolecule: Adds an edge to the graph.
add(MolAtom) - Method in class chemaxon.struc.Sgroup: Adds a new atom to the S-group.
add(CEdge) - Method in class chemaxon.struc.sgroup.SgroupAtom: Add an edge if it had not been already added.
addAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Adds an atom to the list of attachments.
addAttributeKeys(Vector) - Method in class chemaxon.struc.MObject: Adds the attribute names to the specified vector.
addAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MPolyline: Adds the attribute names to the specified vector.
addCdataAttributeKeys(Vector) - Method in class chemaxon.struc.MObject: Adds attribute names to the specified vector.
addCdataAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MTextBox: Adds attribute names to the specified vector.
addChar(char) - Method in class chemaxon.struc.graphics.MTextBox: Adds a character to the text.
addChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup: Adds a child S-group.
addCommand(String, String, Object, String, Class) - Method in class chemaxon.marvin.plugin.CommandPlugger: Adds a plugin.
addEFlowArrows(String, Class) - Method in class chemaxon.marvin.sketch.MObjectPlugger: Adds the electron flow arrow plug-ins.
addEdge0(CEdge) - Method in class chemaxon.struc.CGraph: Adds an edge.
addEdge0(CEdge) - Method in class chemaxon.struc.SelectionMolecule: Adds an edge.
addEdgeWithoutChangingIt(CEdge) - Method in class chemaxon.struc.CGraph: Adds an edge without setting its parentGraph and index fields.
addExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph: Adds explicit lone pairs.
addFolder(String, Class) - Method in class chemaxon.marvin.plugin.CommandPlugger: Adds a plugin folder.
addGraphics(String, Class) - Method in class chemaxon.marvin.sketch.MObjectPlugger: Adds the line, polyline and rectangle plug-ins.
addGraphicsArrow(String, Class) - Method in class chemaxon.marvin.sketch.MObjectPlugger: Adds graphics arrow folder.
addMol(String) - Method in class JMView: Starts loading molecules in a separate thread.
addMol(String, String) - Method in class JMView: Starts loading molecules in a separate thread.
addMol(String) - Method in class MView: Starts loading molecules in a separate thread.
addMol(String, String) - Method in class MView: Starts loading molecules in a separate thread.
addNode0(CNode) - Method in class chemaxon.struc.CGraph: Adds a node.
addNode0(CNode) - Method in class chemaxon.struc.Molecule: Adds a node.
addNode0(CNode) - Method in class chemaxon.struc.SelectionMolecule: Adds a node.
addNodeWithoutChangingIt(CNode) - Method in class chemaxon.struc.CGraph: Adds a node without setting its parentGraph and index fields.
addNotify() - Method in class chemaxon.struc.MObject: Called when the object is added to a document.
addObject(MObject) - Method in class chemaxon.marvin.sketch.modules.RectangleSM
addObject(MObject) - Method in class chemaxon.marvin.sketch.modules.TextBoxSM
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.
addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule: Adds an R-group member.
addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule: Creates a read only RgMolecule from a simple molecule 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.
addString(String) - Method in class chemaxon.struc.graphics.MTextBox: Adds a string to the text.
addStructure(Molecule, int) - Method in class chemaxon.struc.RxnMolecule: Adds a reactant, product or agent.
addStructure(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule: Adds a reactant, product or agent.
adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph: Checks whether the molecule has multiple chiral centres
aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.
aliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.
aliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of aliphatic ring systems of the molecule.
angle2D(double, double) - Method in class chemaxon.struc.DPoint3: Calculates the absolute angle of the vector to the other point on the 2D plane.
animate(String) - Method in class JMView: Starts or stops animation.
animate(String) - Method in class MView: Starts or stops animation.
appendChars(int, char) - Method in class chemaxon.marvin.util.MolExportModule: Append a character n times to the string buffer.
appendLeft(String, int) - Method in class chemaxon.marvin.util.MolExportModule: Append a string to the buffer in %-ns format.
appendMEnd(Molecule) - Method in class chemaxon.marvin.modules.MolExport: Appends the "M END" line to the string buffer.
appendRight(String, int, char) - Method in class chemaxon.marvin.util.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.util.MolExportModule: Append an integer to the buffer in the right hand side of an n-characters wide field.
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.
aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of all aromatic atoms in the molecule.
aromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of all aromatic bonds in the molecule.
aromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of all aromatic ring systems in the molecule (SSSR).
aromatize(int) - Method in class chemaxon.struc.Molecule: Aromatize molecule.
aromatize(boolean) - Method in class chemaxon.struc.MoleculeGraph: Aromatize or dearomatize molecule.
aromatize() - Method in class chemaxon.struc.MoleculeGraph: Aromatize molecule using the default (ChemAxon) aromatization method.
aromatize(int) - Method in class chemaxon.struc.MoleculeGraph: Aromatize molecule.
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.

B

BASIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin: Constant denoting basic pKa.
BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Constant storing the blue rgb value (the basic pKa result color).
BondSM - class chemaxon.marvin.sketch.BondSM.: Bond drawing mode.
BondSM(MolEditor, int) - Constructor for class chemaxon.marvin.sketch.BondSM: Creates a sketcher bond object for the specified molecule editor.
BondSM(MolEditor, MolBond) - Constructor for class chemaxon.marvin.sketch.BondSM: Creates a sketcher bond object for the specified molecule editor.
bondCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of bonds in the molecule including bonds of implicit hydrogens.
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.
bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom: Calculates the average of the bond unit vectors pointing out of this atom.
btab - Variable in class chemaxon.struc.CGraph: Bond table.
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.AtomSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.BondSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.MObjectSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.MoleculeSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.RubberSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.SelectSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.SgroupSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.SketchMode
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.modules.LineSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.modules.RectangleSM
buttonDown(boolean, int) - Method in class chemaxon.marvin.sketch.modules.TextBoxSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.AtomSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.BondSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.MObjectSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.MoleculeSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.RubberSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.SelectSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.SgroupSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.SketchMode
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.modules.LineSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.modules.RectangleSM
buttonUp(int, boolean) - Method in class chemaxon.marvin.sketch.modules.TextBoxSM

C

CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Calculator rgb offset.
CCLENGTH - Static variable in class chemaxon.struc.MolBond: Default bond length.
CEdge - class chemaxon.struc.CEdge.: Edge in a chemical graph.
CEdge(CNode, CNode) - Constructor for class chemaxon.struc.CEdge: Create an edge between two nodes.
CEdge(CEdge) - Constructor for class chemaxon.struc.CEdge: Copy constructor.
CGraph - class chemaxon.struc.CGraph.: Chemical graph.
CGraph(CGraph, int, int) - Constructor for class chemaxon.struc.CGraph: Constructs a fragment with the specified number of nodes and edges
CGraph(CGraph) - Constructor for class chemaxon.struc.CGraph: Constructs a chemical graph.
CGraph() - Constructor for class chemaxon.struc.CGraph: Constructs a chemical graph.
CHARGED_H - Static variable in class chemaxon.struc.MolAtom: Include charged Hydrogen atom(s).
CHART - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Calculation domain type: calculation can be represented in a chart.
CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants: R/S shown always.
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.
CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants: Chirality mask in flags.
CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of R configuration.
CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of S configuration.
CIS - Static variable in interface chemaxon.struc.StereoConstants: Cis double bond.
CLOSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline: Closed flag.
CNode - class chemaxon.struc.CNode.: Node in a chemical graph.
CNode() - Constructor for class chemaxon.struc.CNode
COMPLETE - Static variable in class chemaxon.marvin.modules.AutoMapper: all atoms in the reaction are mapped
COMPRESS - Static variable in class chemaxon.formats.MdlCompressor: This flag must be specified for compression.
CTUMASK - Static variable in interface chemaxon.struc.StereoConstants: Double bond stereo mask.
CTUNKNOWN - Static variable in interface chemaxon.struc.StereoConstants: CIS/TRANS cannot be determined because bond angle is close to 180 degrees.
CTUNSPEC - Static variable in interface chemaxon.struc.StereoConstants: Unspecified double bond.
CTransform3D - class chemaxon.struc.CTransform3D.: 3D transformation matrix.
CTransform3D(CTransform3D) - Constructor for class chemaxon.struc.CTransform3D: Copy constructor.
CTransform3D() - Constructor for class chemaxon.struc.CTransform3D: Constructs an identity transformation.
CalculatorPlugin - class chemaxon.marvin.plugin.CalculatorPlugin.: Common base class for calculator plugins.
CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
CalculatorPluginLoader - class chemaxon.marvin.plugin.CalculatorPluginLoader.: Ancestor of Marvin plugin loaders.
CalculatorPluginLoader() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginLoader
ChargePlugin - class chemaxon.marvin.calculations.ChargePlugin.: Plugin class for charge calculation.
ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin: Constructor.
CommandPlugger - class chemaxon.marvin.plugin.CommandPlugger.: Plugin handler superclass with the ability to store the localized menu labels and a module name for each plugin.
CommandPlugger() - Constructor for class chemaxon.marvin.plugin.CommandPlugger: Constructs an empty plugger.
cacheMemory - Variable in class chemaxon.struc.CGraph
calcCenter() - Method in class chemaxon.struc.MDocument: Calculates the geometrical center.
calcCenter(DPoint3) - Method in class chemaxon.struc.MObject: Calculates the geometrical center.
calcCenter(DPoint3) - Method in class chemaxon.struc.MPoint: 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) - Method in class chemaxon.struc.graphics.MChemicalStruct: Calculates the geometrical center.
calcCenter(DPoint3) - Method in class chemaxon.struc.graphics.MPolyline: Calculates the geometrical center.
calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph: Calculates the graph invariants with the assumption that hydrogens are removed.
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.
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.
calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
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.
calcWidth() - Method in class chemaxon.struc.MoleculeGraph: Calculates the molecule width.
calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the logD value at fixed pH.
canBeAbbrevgroup(String) - Static method in class chemaxon.formats.MolInputStream: Utility function that checks if a string can be in abbrevgroup format.
canBeBase64(String) - Static method in class chemaxon.formats.MolInputStream: Utility function that checks if a string can be base64 encoded data.
canBeCT(int, int) - Method in class chemaxon.struc.MoleculeGraph: Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
canBeChime(String) - Static method in class chemaxon.formats.MolInputStream: Utility function that checks if a string can be Chime (MDL compressed mol).
canBeJTF(String) - Static method in class chemaxon.formats.MolInputStream: Determines if a String is valid as the first line of a JTF file.
canBeSMARTS(String) - Static method in class chemaxon.formats.MolInputStream: Utility function that checks if a string can be SMARTS.
canBeSMILES(String) - Static method in class chemaxon.formats.MolInputStream: Utility function that checks if a string can be SMILES.
canPointToAtom() - Method in class chemaxon.marvin.sketch.AtomSM: Can the user point to an atom in this sketching mode?
canPointToAtom() - Method in class chemaxon.marvin.sketch.BondSM: Can the user point to an atom in this sketching mode?
canPointToAtom() - Method in class chemaxon.marvin.sketch.RubberSM: Can the user point to an atom in this sketching mode?
canPointToAtom() - Method in class chemaxon.marvin.sketch.SelectSM: Can the user point to an atom in this sketching mode?
canPointToAtom() - Method in class chemaxon.marvin.sketch.SgroupSM: Can the user point to an atom in this sketching mode?
canPointToAtom() - Method in class chemaxon.marvin.sketch.SketchMode: Can the user point to an atom in this sketching mode?
canPointToAtom() - Method in class chemaxon.marvin.sketch.modules.LineSM: Can the user point to an atom in this sketching mode?
canPointToAtomPair() - Method in class chemaxon.marvin.sketch.SketchMode: Can the user point to an atom pair in this sketching mode?
canPointToAtomPair() - Method in class chemaxon.marvin.sketch.modules.EFlowSM: The user can point to an atom pair with the end of the arrow.
canPointToBond() - Method in class chemaxon.marvin.sketch.AtomSM: Can the user point to a bond in this sketching mode?
canPointToBond() - Method in class chemaxon.marvin.sketch.BondSM: Can the user point to a bond in this sketching mode?
canPointToBond() - Method in class chemaxon.marvin.sketch.RubberSM: Can the user point to a bond in this sketching mode?
canPointToBond() - Method in class chemaxon.marvin.sketch.SelectSM: Can the user point to a bond in this sketching mode?
canPointToBond() - Method in class chemaxon.marvin.sketch.SketchMode: Can the user point to a bond in this sketching mode?
canPointToBond() - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Can the user point to a bond in this sketching mode?
canPointToBond() - Method in class chemaxon.marvin.sketch.modules.LineSM: Can the user point to a bond in this sketching mode?
canPointToMObject() - Method in class chemaxon.marvin.sketch.MObjectSM: Can the user point to a graphics object in this sketching mode?
canPointToMObject() - Method in class chemaxon.marvin.sketch.RubberSM: Can the user point to a graphics object in this sketching mode?
canPointToMObject() - Method in class chemaxon.marvin.sketch.SelectSM: Can the user point to a graphics object in this sketching mode?
canPointToMObject() - Method in class chemaxon.marvin.sketch.SketchMode: Can the user point to a graphics object in this sketching mode?
canPointToMObject() - Method in class chemaxon.marvin.sketch.modules.LineSM: Can the user point to another graphics object in this sketching mode?
canPointToSgroup() - Method in class chemaxon.marvin.sketch.AtomSM: Can the user point to an S-group in this sketching mode?
canPointToSgroup() - Method in class chemaxon.marvin.sketch.BondSM: Can the user point to an S-group in this sketching mode?
canPointToSgroup() - Method in class chemaxon.marvin.sketch.RubberSM: Can the user point to an S-group in this sketching mode?
canPointToSgroup() - Method in class chemaxon.marvin.sketch.SelectSM: Can the user point to an S-group in this sketching mode?
canPointToSgroup() - Method in class chemaxon.marvin.sketch.SgroupSM: Can the user point to an S-group in this sketching mode?
canPointToSgroup() - Method in class chemaxon.marvin.sketch.SketchMode: Can the user point to an S-group in this sketching mode?
chainAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of chain atoms in the molecule excluding hydrogens.
chainBondCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.
check() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Protects plugin license.
checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Increases the call counter if no valid license exists for this plugin class.
checkLicenseKey() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Checks the license key.
checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: 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.MajorMicrospeciesPlugin: 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.TPSAPlugin: 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.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.pKaPlugin: 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 occurence range string for syntax errors and returns a "normalized" string.
checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Checks result types.
checkValidity(MDocument, Vector) - Method in class chemaxon.struc.MObject: Is it a valid object in the document?
checkValidity(MDocument, Vector) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Is it a valid object in the document?
checkValidity(MDocument, Vector) - Method in class chemaxon.struc.graphics.MPolyline: Is it a valid object in the document?
chemaxon.calculations - package chemaxon.calculations: Contains chemical computations modules.
chemaxon.formats - package chemaxon.formats: Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.
chemaxon.marvin.calculations - package chemaxon.marvin.calculations: Provides specific plugin, plugin loader and table form output implementations.
chemaxon.marvin.modules - package chemaxon.marvin.modules: Marvin modules.
chemaxon.marvin.plugin - package chemaxon.marvin.plugin: Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.
chemaxon.marvin.sketch - package chemaxon.marvin.sketch: Contains the sketcher's core classes and various sketching modes.
chemaxon.marvin.sketch.modules - package chemaxon.marvin.sketch.modules: Contains sketcher modules.
chemaxon.marvin.util - package chemaxon.marvin.util: Contains the fundamental classes for molecule import and export.
chemaxon.struc - package chemaxon.struc: Provides classes for implementing and manipulating chemical structures.
chemaxon.struc.graphics - package chemaxon.struc.graphics: Contains graphics MDocument elements.
chemaxon.struc.sgroup - package chemaxon.struc.sgroup: S-group related classes and interfaces.
clean(int, String, ProgressObserver) - Method in class chemaxon.struc.Molecule: Calculates atom coordinates.
clean(int, String) - Method in class chemaxon.struc.MoleculeGraph: Calculates atom coordinates.
clean(int, String, ProgressObserver) - Method in class chemaxon.struc.MoleculeGraph: Calculates atom coordinates.
clear() - Method in class chemaxon.marvin.plugin.CommandPlugger: Removes all plugins.
clear() - Method in class chemaxon.struc.MDocument: Clears the document.
clear() - Method in class chemaxon.struc.MSelectionDocument: 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.
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 edges 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.
clearProperties() - Method in class chemaxon.struc.Molecule: Clears RDfile/SDfile properties.
clearProperties() - Method in class chemaxon.struc.RgMolecule: Clears RDfile/SDfile properties in the root structure.
clearQProps() - Method in class chemaxon.struc.MolAtom: Clears query props.
clickPoint - Variable in class chemaxon.marvin.sketch.modules.RectangleSM
clone() - Method in class chemaxon.marvin.sketch.AtomSM
clone() - Method in class chemaxon.marvin.sketch.BondSM
clone() - Method in class chemaxon.marvin.sketch.MObjectSM: Clones the object.
clone() - Method in class chemaxon.marvin.sketch.MoleculeSM
clone() - Method in class chemaxon.marvin.sketch.RubberSM: Clones the selection object.
clone() - Method in class chemaxon.marvin.sketch.SelectSM: Clones the selection object.
clone() - Method in class chemaxon.marvin.sketch.SgroupSM: Clones the selection object.
clone() - Method in class chemaxon.marvin.sketch.SketchMode
clone() - Method in class chemaxon.marvin.sketch.modules.ArrowSM
clone() - Method in class chemaxon.marvin.sketch.modules.EFlow1SM
clone() - Method in class chemaxon.marvin.sketch.modules.EFlowSM
clone() - Method in class chemaxon.marvin.sketch.modules.LineSM
clone() - Method in class chemaxon.marvin.sketch.modules.PolylineSM
clone() - Method in class chemaxon.marvin.sketch.modules.RectangleSM: Clones the object.
clone() - Method in class chemaxon.marvin.sketch.modules.TextBoxSM: Clones the object.
clone() - Method in class chemaxon.struc.CEdge: Clones this edge.
clone() - Method in class chemaxon.struc.CGraph: Makes an identical copy of the molecule.
clone() - Method in class chemaxon.struc.CNode: Clones the node.
clone() - Method in class chemaxon.struc.DPoint3: Make an identical copy.
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.MPoint
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: Make 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.SelectionMolecule: Create a clone of the selection.
clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint
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.MPolyline
clone() - Method in class chemaxon.struc.graphics.MRectangle
clone() - Method in class chemaxon.struc.graphics.MTextBox
clone() - Method in class chemaxon.struc.sgroup.SgroupAtom: Clones the S-group superatom.
cloneArrowSM() - Method in class chemaxon.marvin.sketch.modules.ArrowSM.Regular
cloneArrowSM() - Method in class chemaxon.marvin.sketch.modules.ArrowSM.TwoHeaded
cloneArrowSM() - Method in class chemaxon.marvin.sketch.modules.ArrowSM
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.
cloneMainMolecule() - Method in class chemaxon.struc.MDocument: Creates a clone.
cloneMainMoleculeGraph() - Method in class chemaxon.struc.MDocument: Creates a clone.
cloneMol(Molecule) - Static method in class chemaxon.marvin.sketch.MoleculeSM
cloneMolecule() - Method in class chemaxon.struc.Molecule: Make an identical copy of the molecule.
cloneMolecule() - Method in class chemaxon.struc.RgMolecule: Make an identical copy of the molecule.
cloneMolecule() - Method in class chemaxon.struc.RxnMolecule: Make an identical copy of the molecule.
cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.Sgroup: Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets a new Sgroup instance.
cloneSgroup(Molecule, Sgroup) - 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.
clonecopy(CGraph) - Method in class chemaxon.struc.CGraph: Copies the clones of nodes and edges of this graph to another one.
clonecopy(CGraph) - Method in class chemaxon.struc.Molecule: Make another molecule identical to this one.
clonecopy(CGraph) - Method in class chemaxon.struc.MoleculeGraph: Make another molecule identical to this one.
clonecopy(CGraph) - Method in class chemaxon.struc.RgMolecule: Make another molecule identical to this one.
clonecopy(CGraph) - Method in class chemaxon.struc.RxnMolecule: Make another molecule identical to this one.
clonecopy(CGraph) - Method in class chemaxon.struc.SelectionMolecule: Copies the clones of nodes and edges of this graph to another one.
clonecopyWithoutSgroups(Molecule) - Method in class chemaxon.struc.Molecule: Copy the all the contents except the S-groups into another molecule object.
clonelesscopy(CGraph) - Method in class chemaxon.struc.CGraph: Copy to selection.
clonelesscopy(CGraph) - Method in class chemaxon.struc.Molecule: Copy to selection.
clonelesscopy(CGraph) - Method in class chemaxon.struc.MoleculeGraph: Copy to selection.
clonelesscopy(CGraph) - Method in class chemaxon.struc.RgMolecule: Copy to selection.
clonelesscopy(CGraph) - Method in class chemaxon.struc.RxnMolecule: Copy to selection.
close() - Method in class chemaxon.marvin.util.MolExportModule: Close the stream.
composition(int) - Method in class chemaxon.calculations.ElementalAnalyser: Gets the molecular composition (w/w%).
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.AtomSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.BondSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.MObjectSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.MoleculeSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.RubberSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.SelectSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.SgroupSM
containedObjectEquals(SketchMode) - Method in class chemaxon.marvin.sketch.SketchMode
contains(Object) - Method in class chemaxon.struc.CGraph: Checks if the graph contains the specified node or edge.
contains(CGraph) - Method in class chemaxon.struc.CGraph: Does the graph contain the specified fragment?
contains(MObject) - Method in class chemaxon.struc.MDocument: Searches an object in the document.
contains(MDocument) - Method in class chemaxon.struc.MDocument: Checks if the document contains all objects of another document or not.
contains(CGraph) - Method in class chemaxon.struc.MoleculeGraph: Does the graph contain the specified fragment?
contains(Object) - Method in class chemaxon.struc.RgMolecule: Checks if the root structure or an R-group contains the specified node or edge.
contains(Object) - Method in class chemaxon.struc.RxnMolecule: Checks if a reactant, agent or product structure contains the specified node or edge.
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.MObject: Checks if the object contains the specified atom reference.
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.MPolyline: Checks if the atom set contains the specified atom object.
containsOnlyOne(Class) - Method in class chemaxon.struc.MDocument: Checks if the document contains only whan object of the specified class.
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.
contractSgroups() - Method in class chemaxon.struc.Molecule: Contracts all S-groups.
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(Molecule) - Method in class chemaxon.marvin.modules.MolExport: Creates an MDL mol or compressed mol representation of the molecule.
convert(Molecule) - Method in class chemaxon.marvin.util.MolExportModule: Convert a molecule to a string or byte array.
convertToFrags() - Method in class chemaxon.struc.Molecule: Converts this molecule to its disconnected fragments.
copy(CNode) - Method in class chemaxon.struc.MolAtom: Make a copy of this atom.
copy(CNode) - Method in class chemaxon.struc.sgroup.SgroupAtom: Make a copy of this S-group superatom.
copyFromSgroupCopy(SgroupAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom: Make a copy of this S-group superatom.
copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline: Copies line properties to another line object.
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.
covalentRadiusOf(int, int) - Static method in class chemaxon.struc.MolAtom: Gets the covalent radius in C-C bond length units.
create(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin: Creates a CalculatorPlugin object.
createBHtab() - Method in class chemaxon.struc.MoleculeGraph: Creates the bond table extended with implicit hydrogen atoms.
createBHtab() - Method in class chemaxon.struc.RxnMolecule: Creates the graph union's bond table extended with implicit hydrogen atoms.
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.
createDehydrogenizedReadOnlyGraph() - Method in class chemaxon.struc.MoleculeGraph: Creates a dehydrogenized version of the molecule.
createImageMolecule() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Transforms molecule 'origmol' for molecule image purpose.
createLine(MPoint, MPoint) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Creates a line object.
createLine(MPoint, MPoint) - Method in class chemaxon.marvin.sketch.modules.LineSM: Creates a line object.
createMol() - Method in class chemaxon.marvin.modules.MolImport: Creates a new target molecule object.
createMol() - Method in interface chemaxon.marvin.util.MolImportIface: Creates a new target molecule object for the import.
createMol(String) - Static method in class chemaxon.struc.RgMolecule: Deprecated. As of Marvin 3.4, MolImportIface.createMol() must be used.
createMolecule() - Method in class chemaxon.struc.Sgroup: Creates a molecule object that contains only this group.
createMolecule() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Creates a molecule object that contains only this group.
createPolyline(MPolyline, MPoint) - Method in class chemaxon.marvin.sketch.modules.LineSM: Creates a polyline object.
createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule: Creates a reaction.
createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Creates standardized molecule, the original input molecule is cloned.
ctab - Variable in class chemaxon.struc.CGraph: Connection table.
cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox: Move the cursor down.
cursorUp(boolean) - Method in class chemaxon.struc.graphics.MTextBox: Moves the cursor up.

D

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.
DEFAULT_OPTIONS - Static variable in interface chemaxon.struc.sgroup.Expandable: Default expansion/contraction options.
DEFAULT_THICKNESS - Static variable in class chemaxon.struc.graphics.MPolyline: Default line thickness.
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
DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph: Dimension bits in flags.
DONOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin: Donor sign displayed in GUI.
DOUBLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond: Double or aromatic query bond type.
DOWN - Static variable in class chemaxon.struc.MolBond: Single bond down.
DPoint3 - class chemaxon.struc.DPoint3.: 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.
dearomatize() - Method in class chemaxon.struc.Molecule: Dearomatize molecule.
dearomatize() - Method in class chemaxon.struc.MoleculeGraph: Dearomatize molecule.
dehydrogenize(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin: Makes all explicit H-s implicit.
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).
desiredLength(int, int, int, int) - Static method in class chemaxon.struc.MolBond: Desired length of a bond between two atoms in Angstroms.
destroy() - Method in class JMSketch: Dispose all the frames.
destroy() - Method in class JMView: Dispose all the frames.
destroy() - Method in class MSketch: Remove all the components, dispose all the frames.
destroy() - Method in class MView: Dispose all the frames.
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) - Method in class chemaxon.struc.RxnMolecule: Determines whether a point should be in a reactant, in a product or in an agent.
distance(DPoint3) - Method in class chemaxon.struc.DPoint3: Calculates the distance between two points.
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.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets the 2D distance from the specified point.
distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline: Gets the 2D distance from the specified point.
draw(Graphics, String) - Method in class chemaxon.struc.Molecule: Draws the molecule into a graphics context.
dump() - Method in class chemaxon.marvin.modules.AutoMapper: Engineering function.

E

EFlow1SM - class chemaxon.marvin.sketch.modules.EFlow1SM.: Electron flow arrow drawing mode for one-electron transfer.
EFlow1SM() - Constructor for class chemaxon.marvin.sketch.modules.EFlow1SM: Creates an electron flow sketch mode object.
EFlow1SM(EFlow1SM) - Constructor for class chemaxon.marvin.sketch.modules.EFlow1SM: Copy constructor.
EFlowSM - class chemaxon.marvin.sketch.modules.EFlowSM.: Electron flow arrow drawing mode.
EFlowSM() - Constructor for class chemaxon.marvin.sketch.modules.EFlowSM: Creates an electron flow sketch mode object.
EFlowSM(EFlowSM) - Constructor for class chemaxon.marvin.sketch.modules.EFlowSM: Copy constructor.
EFlowSM(int) - Constructor for class chemaxon.marvin.sketch.modules.EFlowSM: Creates an electron flow sketch mode object.
ELEMENT_COUNT - Static variable in class chemaxon.struc.MolAtom: Number of elements in the periodic system
EMPTY - Static variable in class chemaxon.struc.MolAtom: Empty atom type.
EPSILON - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
EPSILON - Static variable in class chemaxon.marvin.calculations.pKaPlugin: The microspecies is ignored if its distribution is less than EPSILON for all pH values.
E_SINK - Static variable in class chemaxon.struc.graphics.MEFlow: Electron sink.
E_SOURCE - Static variable in class chemaxon.struc.graphics.MEFlow: Electron source.
ElementalAnalyser - class chemaxon.calculations.ElementalAnalyser.: Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyser() - Constructor for class chemaxon.calculations.ElementalAnalyser
ElementalAnalyserPlugin - class chemaxon.marvin.calculations.ElementalAnalyserPlugin.: Calculates molecular formula, mass, MS mass and composition.
ElementalAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.ElementalAnalyserPlugin
Expandable - interface chemaxon.struc.sgroup.Expandable.: Expandable interface for S-groups.
edgeCount - Variable in class chemaxon.struc.CGraph: The number of edges.
edges - Variable in class chemaxon.struc.CGraph: The edges (bonds).
edges - Variable in class chemaxon.struc.CNode: The edges.
electronegOf(int) - Static method in class chemaxon.struc.MolAtom: Gets 10 times the electronegativity value for the specified element.
endReuse(int) - Method in class chemaxon.struc.Molecule: End reusing atoms.
endReuse(int) - Method in class chemaxon.struc.RgMolecule: End reusing atoms.
equals(Object) - Method in class chemaxon.struc.CEdge: Two edges equal if their endpoints are the same.
equals(Object) - Method in class chemaxon.struc.DPoint3: Two points equal if their coordinates equal.
equals(MPoint) - Method in class chemaxon.struc.MPoint: Two points equal if their location equals.
equals(Object) - Method in class chemaxon.struc.MPoint: Two points equal if their location equals.
equals(MAtomSetPoint) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Two points equal if their atoms equal.
equals(MPoint) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Two points equal if their atoms equal.
equals(Object) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Two points equal if their atoms equal.
exactMass() - Method in class chemaxon.calculations.ElementalAnalyser: Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
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.
expand(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Expands this S-group.
expandSgroups() - Method in class chemaxon.struc.Molecule: Expands all S-groups.
expandSgroups(int) - Method in class chemaxon.struc.Molecule: Expands all S-groups.

F

FIX_CHARGE - Static variable in class chemaxon.struc.MolAtom: The charge is fix if this flag is set.
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.
findAtomClone(MolAtom) - Method in class chemaxon.struc.MoleculeGraph: Finds the clone of an 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.SuperatomSgroup: Finds the crossing bonds.
findEdge(CEdge) - Method in class chemaxon.struc.CGraph: Finds an edge in the edgess array.
findExpandableSgroup() - Method in class chemaxon.struc.Molecule: Finds a contracted residue.
findFrag(int, CGraph) - Method in class chemaxon.struc.CGraph: Determines the subgraph connected to the specified node.
findFrags(Class) - Method in class chemaxon.struc.CGraph: Determines the disconnected fragments and puts them into an array.
findFrags() - Method in class chemaxon.struc.Molecule: Determines the disconnected fragments and puts them into an array.
findNode(CNode) - Method in class chemaxon.struc.CGraph: Finds a node in the nodes array.
findRgroupIndex(int) - Method in class chemaxon.struc.RgMolecule: Finds R-group R#.
findSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Finds the largest S-group that contains the specified node.
findSgroupOf(MolAtom) - Method in class chemaxon.struc.Molecule: Finds the smallest S-group related to the specified node.
findSmallestSgroupContaining(MolAtom) - Method in class chemaxon.struc.Molecule: Finds the smallest S-group that contains the specified node.
findSmallestSgroupContaining(MolAtom) - Method in class chemaxon.struc.Sgroup: Finds the smallest S-group containing the specified node.
findSmallestSgroupOf(MolAtom) - Method in class chemaxon.struc.Sgroup: Finds the smallest S-group that has the specified node.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.MObject: Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Finish cloning a document.
finishCloning(MDocument, MDocument) - Method in class chemaxon.struc.graphics.MPolyline: Finish cloning a document.
flags - Variable in class chemaxon.struc.MoleculeGraph: Stores the dimension (0, 2 or 3) and the chiral flag.
format(double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Converts a double into String, applying the maximum number of fractional digits specified.
format(double, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Converts a double into String, applying the maximum number of fractional digits specified.
format(double, StringBuffer) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Converts a double into String, applying the maximum number of fractional digits specified.
format(double[][], int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Converts a double[][] 2xN table to a 2-column tab-separated string representation of the table.
formula() - Method in class chemaxon.calculations.ElementalAnalyser: Gets the molecular formula.
fragIds - Variable in class chemaxon.struc.CGraph: Fragment identifiers.
fuse(CGraph) - Method in class chemaxon.struc.CGraph: Adds those nodes and edges of a graph to this one that are not already elements.
fuse(CGraph) - Method in class chemaxon.struc.RgMolecule: Add the atoms and bonds of another molecule.
fuse(CGraph) - Method in class chemaxon.struc.RxnMolecule: Add the atoms and bonds of another molecule.
fuse0(CGraph) - Method in class chemaxon.struc.CGraph: Adds those nodes and edges of a graph to this one that are not already elements.
fuse0(CGraph) - Method in class chemaxon.struc.RgMolecule: Add those nodes and edges of a graph that are not already elements.
fuse0(CGraph) - Method in class chemaxon.struc.RxnMolecule: Add those nodes and edges of a graph that are not already elements.
fuse0(CGraph) - Method in class chemaxon.struc.SelectionMolecule: Adds those nodes and edges of a graph to this one that are not already elements.
fusedAliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
fusedAromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
fusedRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.

G

getAbundance(int, int) - Static method in class chemaxon.struc.PeriodicSystem: Natural abundance of the isotope
getAcceptorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the overall acceptor atom count (without multiplicity) in the molecule.
getAcceptorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the atomic acceptor count corresponding to the specified atom index.
getAcceptorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the overall acceptor count (with multiplicity) in the molecule.
getAgent(int) - Method in class chemaxon.struc.RxnMolecule: Gets an agent.
getAgentCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of agents.
getAliasstr() - Method in class chemaxon.struc.MolAtom: Gets the alias string.
getAliphaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the aliphatic atom count.
getAliphaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the aliphatic bond count.
getAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the aliphatic ring count.
getAllAtomCount() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the atom count (including implicit hydrogens).
getAllAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the atom count.
getAppletInfo() - Method in class JMSketch: Returns a string containing the version and the author.
getAppletInfo() - Method in class JMView: Returns a string containing the version and the author.
getAppletInfo() - Method in class MSketch: Returns a string containing the version and the author.
getAppletInfo() - Method in class MView: Returns a string containing the version and the author.
getArcAngle() - Method in class chemaxon.struc.graphics.MPolyline: Gets the central angle of the arc.
getArcCenter(DPoint3, DPoint3, double) - Static method in class chemaxon.struc.graphics.MPolyline: Returns the arc center.
getArcRadius() - Method in class chemaxon.struc.graphics.MPolyline: Gets the arc radius.
getAromaticAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the aromatic atom count.
getAromaticBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the aromatic bond count.
getAromaticRingCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the total partial charge of the smallest aromatic ring containing the specified atom.
getAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the aromatic ring count.
getAromaticSystemCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the total partial charge of the aromatic system containing the specified atom.
getAromrings() - Method in class chemaxon.struc.MoleculeGraph: Get aromatic ring atom indexes.
getAromrings(int) - Method in class chemaxon.struc.MoleculeGraph: Get aromatic ring atom indexes.
getArrowFlags(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arrow flags.
getArrowLength(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arrow head length.
getArrowWidth(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the arrow head width.
getAtno() - Method in class chemaxon.struc.MolAtom: Gets the atomic number.
getAtom() - Method in class chemaxon.marvin.sketch.AtomSM: Gets the atom.
getAtom(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the nth atom.
getAtom(int) - Method in class chemaxon.struc.Sgroup: Gets an atom in the S-group.
getAtom1() - Method in class chemaxon.struc.MolBond: Gets the first endpoint.
getAtom2() - Method in class chemaxon.struc.MolBond: Gets the second endpoint.
getAtomAlias(int) - Method in class JMSketch: Gets atom alias.
getAtomAlias(int, int) - Method in class JMView: Gets atom alias.
getAtomAlias(int) - Method in class MSketch: Gets atom alias.
getAtomAlias(int, int) - Method in class MView: Gets atom alias.
getAtomArray() - Method in class chemaxon.struc.MoleculeGraph: Creates an array of atoms.
getAtomArray() - Method in class chemaxon.struc.Sgroup: Gets the array of atoms in the S-group.
getAtomCount() - Method in class JMSketch: Returns the number of atoms.
getAtomCount(int) - Method in class JMView: Gets the number of atoms in the specified molecule cell.
getAtomCount() - Method in class MSketch: Returns the number of atoms.
getAtomCount(int) - Method in class MView: Gets the number of atoms in the specified molecule cell.
getAtomCount(int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the number of atoms with given atomic number.
getAtomCount(int, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the number of atoms with given atomic number in the molecule isotope with the specified mass number.
getAtomCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the number of atoms in the input molecule.
getAtomCount() - Method in class chemaxon.struc.MoleculeGraph: Gets the number of atoms.
getAtomCount() - Method in class chemaxon.struc.Sgroup: Gets the number of atoms in the S-group.
getAtomExtraLabel(int) - Method in class JMSketch: Gets extra atom label.
getAtomExtraLabel(int, int) - Method in class JMView: Gets extra atom label.
getAtomExtraLabel(int) - Method in class MSketch: Gets extra atom label.
getAtomExtraLabel(int, int) - Method in class MView: Gets extra atom label.
getAtomIndex(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the atom index in the standardized molecule, or the atom index itself if the input molecule has not been standardized.
getAtomMap() - Method in class chemaxon.struc.MolAtom: Gets the atom-atom mapping number.
getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.MolAtom: Gets the string representation of the atom symbol.
getAtomSymbol(int, int, int[], CTransform3D) - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the string representation of the atom symbol.
getAtomicNumber(String) - Static method in class chemaxon.struc.PeriodicSystem: Returns the atomic number of the element specified by its symbol.
getAtomlogPIncrement(int) - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the logP increment for the specified atom.
getAtoms() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the atoms.
getAttach() - Method in class chemaxon.struc.MolAtom: Gets attachment point information.
getAttachAtom(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets an attachment point.
getAttribute(String) - Method in class chemaxon.struc.MObject: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MPolyline: Gets the value of an attribute.
getAttribute(String) - Method in class chemaxon.struc.graphics.MTextBox: Gets the value of an attribute.
getAutoScale() - Method in class JMSketch: Returns the autoscale property.
getAutoScale() - Method in class MSketch: Returns the autoscale property.
getAveragePolarizabilityComponent() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the average polarizability component (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
getBackground() - Method in class chemaxon.struc.MObject: Gets the background color of the object.
getBestTabScale(int) - Method in class JMView: Gets the best scale value for a molecule cell.
getBestTabScale() - Method in class JMView: Gets the smallest best scale value in the molecule table.
getBestTabScale(int) - Method in class MView: Gets the best scale value for a molecule cell.
getBestTabScale() - Method in class MView: Gets the smallest best scale value in the molecule table.
getBond(int) - Method in class chemaxon.struc.MolAtom: Gets the i-th bond.
getBond(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the nth bond.
getBondArray() - Method in class chemaxon.struc.MoleculeGraph: Creates an array of bonds.
getBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the bond count.
getBondCount() - Method in class chemaxon.struc.MolAtom: Gets the number of bonds/ligands.
getBondCount() - Method in class chemaxon.struc.MoleculeGraph: Gets the number of bonds.
getBtab() - Method in class chemaxon.struc.CGraph: Gets the edge (bond) table.
getBtab() - Method in class chemaxon.struc.RgMolecule: Gets the bond table of the root structre.
getBtab() - Method in class chemaxon.struc.RxnMolecule: Gets the bond table for the graph union.
getC(int) - Method in class JMView: Gets the state of a checkbox.
getC(int) - Method in class MView: Gets the state of a checkbox.
getCTAtom1() - Method in class chemaxon.struc.MolBond: Gets the first atom for cis/trans stereo calculation.
getCTAtom4() - Method in class chemaxon.struc.MolBond: Gets the fourth atom for cis/trans stereo calculation.
getCellCount() - Method in class JMView: Gets the number of cells in the table.
getCellCount() - Method in class MView: Gets the number of cells in the table.
getCenter(int, int) - Method in class chemaxon.struc.RxnMolecule: Gets the geometrical center of a reaction component.
getChainAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the chain atom count.
getChainBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the chain bond count.
getCharge() - Method in class chemaxon.struc.MolAtom: Gets the charge.
getChartColor(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the chart colors to be displayed in msketch/mview GUI.
getChartColor(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the chart colors to be displayed in msketch/mview GUI.
getChartLabel() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the chart checkbox label.
getChartTitle() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the chart title.
getChildSgroup(int) - Method in class chemaxon.struc.Sgroup: Gets a child S-group.
getChildSgroupCount() - Method in class chemaxon.struc.Sgroup: Gets the number of child S-groups.
getChirality(int) - Method in class chemaxon.struc.MoleculeGraph: Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
getClipObject(CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle: Gets the clipping rectangle.
getColor() - Method in class chemaxon.struc.MObject: Gets the color of the object.
getCommand(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets a command.
getCommand(MObject) - Method in class chemaxon.marvin.sketch.MObjectPlugger: Gets the sketch command for a graphics object.
getCommandCount() - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the number of commands (plugins).
getCommandFolder(String) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the folder name for a command.
getCommandIcon(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the small icon for a command.
getCommandLabel(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the menu item label for a command.
getCommandPluggerClass(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the class of the plugger the specified plugin corresponds to.
getCommandPluggerRC(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the resource bundle of the plugger the specified plugin corresponds to.
getComment() - Method in class chemaxon.struc.Molecule: Gets the comment.
getComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the molecule formula composition.
getConnectivity() - Method in class chemaxon.struc.Sgroup: Gets S-group connectivity.
getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.Sgroup: Gets the atoms that have crossing bonds.
getCrossingAtoms(MolBond[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the atoms that have crossing bonds.
getCtab() - Method in class chemaxon.struc.CGraph: Gets the connection table.
getCtab() - Method in class chemaxon.struc.RgMolecule: Gets the connection table of the root structure.
getCtab() - Method in class chemaxon.struc.RxnMolecule: Gets the connection table for the graph union.
getCursorPos() - Method in class chemaxon.struc.graphics.MTextBox: Gets the cursor position.
getDesiredLength(int, int, int) - Method in class chemaxon.struc.MoleculeGraph: Gets the ideal bond length in Angstroms.
getDesiredLength(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Gets the ideal bond length in Angstroms.
getDim() - Method in class chemaxon.struc.MoleculeGraph: Gets the dimension.
getDocument() - Method in class chemaxon.struc.MoleculeGraph: Gets the parent document object.
getDonorAtomCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the overall donor atom count (without multiplicity) in the molecule.
getDonorCount(int) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the atomic donor count corresponding to the specified atom index.
getDonorCount() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the overall donor count (with multiplicity) in the molecule.
getDoublePrecision() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the precision.
getDraggedObject() - Method in class chemaxon.struc.MDocument: Gets the dragged object
getEFlow() - Method in class chemaxon.marvin.sketch.modules.EFlowSM
getEdge(int) - Method in class chemaxon.struc.CGraph: Gets an edge.
getEdge(int) - Method in class chemaxon.struc.CNode: Gets the i-th edge.
getEdge(int) - Method in class chemaxon.struc.RgMolecule: Gets an edge of the root structure.
getEdge(int) - Method in class chemaxon.struc.RxnMolecule: Gets an edge.
getEdgeArray() - Method in class chemaxon.struc.CGraph: Creates an array of edges.
getEdgeArray() - Method in class chemaxon.struc.MoleculeGraph: Creates an array of bonds.
getEdgeCount() - Method in class chemaxon.struc.CGraph: Gets the number of edges.
getEdgeCount() - Method in class chemaxon.struc.CNode: Gets the number of edges/ligands.
getEdgeCount() - Method in class chemaxon.struc.RgMolecule
getEdgeCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of edges in the graph union.
getEdgeTo(CNode) - Method in class chemaxon.struc.CNode: Finds the edge that connects this node to another node.
getEdgeVector() - Method in class chemaxon.struc.CGraph: Gets the edges.
getEditor() - Method in class chemaxon.marvin.sketch.SketchMode: Gets the molecule editor.
getElectrophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
getElectrophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the electrophilic order of an atom, -1 for no value.
getElementCount() - Static method in class chemaxon.struc.PeriodicSystem: Number of elements in the periodic system
getEndPosition() - Method in class chemaxon.struc.MDocument: Gets the end position of this document in the input file.
getEndPosition() - Method in class chemaxon.struc.Molecule: Gets the end position of this molecule in the input file.
getErrorLevel() - Method in class chemaxon.marvin.plugin.PluginException: Returns the error level.
getErrorMessage() - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the calculation error information message if ChargePlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the calculation error information message if HBDAPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the calculation error information message if IonChargePlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the calculation error information message if MajorMicrospeciesPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the calculation error information message if PolarizabilityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the calculation error information message if RefractivityPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the calculation error information message if TPSAPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the calculation error information message if logDPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the calculation error information message if logPPlugin.run() returned false (calculation error): hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the calculation error information message if pKaPlugin.run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
getErrorMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).
getExactMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the molecule exact mass.
getException() - Method in class chemaxon.marvin.plugin.PluginException: Returns the wrapped exception.
getExplicitHcount() - Method in class chemaxon.struc.MolAtom: Gets number of hydrogen connections.
getExplicitHcount() - Method in class chemaxon.struc.MoleculeGraph: Gets the total number of explicit hydrogens attached to the molecule.
getExtraLabel() - Method in class chemaxon.struc.MolAtom: Gets the label string: "result" or "result1|result2".
getExtraLabelColor() - Method in class chemaxon.struc.MolAtom: Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
getExtraLabelColor(int) - Method in class chemaxon.struc.MolAtom: Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue).
getFilePointer() - Method in class chemaxon.formats.MolInputStream: Get the file pointer.
getFlags() - Method in class chemaxon.struc.MolAtom: Gets flags.
getFlags() - Method in class chemaxon.struc.MolBond: Gets bond type (3 bit), stereo (2+2+1 bit), topology (2 bit) and bond set (5 bit) information.
getFlags() - Method in class chemaxon.struc.graphics.MPolyline: Gets the flags.
getFocus() - Method in class chemaxon.struc.MDocument: Gets the focused object
getFolderCount() - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the number of folders.
getFolderLabel(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the label of a folder.
getFolderLabel(String) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the label of a folder.
getFolderName(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the name of a folder.
getFolderPluggerClass(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the class of the plugger that created the specified folder.
getFolderPluggerRC(int) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the resource bundle of the plugger that created the specified folder.
getFolderPluggerRC(String) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the resource bundle of the plugger that created the specified folder.
getForefather() - Method in class chemaxon.struc.CGraph: Gets the first parent.
getFormat() - Method in class chemaxon.formats.MolInputStream: Get the molecule file format.
getFormat() - Method in class chemaxon.marvin.util.MolExportModule: Returns the output format.
getFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the molecule formula.
getFormula() - Method in class chemaxon.struc.MoleculeGraph: Gets the molecular formula.
getFormula() - Method in class chemaxon.struc.RgMolecule: Gets the molecular formula in Hill order.
getFormula() - Method in class chemaxon.struc.RxnMolecule: Gets the molecular formula in Hill order.
getFragCount() - Method in class chemaxon.struc.CGraph: Returns the number of fragments.
getFragIds() - Method in class chemaxon.struc.CGraph: Gets an array containing the fragment id for each node.
getFreeLegalAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the unused legal attachment points.
getFusedAliphaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
getFusedAromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
getFusedRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.
getGUIResultTypes() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the result types to be displayed in msketch/mview GUI.
getGUIResultTypes() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the result types to be displayed in msketch/mview GUI.
getGraphUnion() - Method in class chemaxon.struc.MoleculeGraph: Gets a graph containing all the atoms and bonds.
getGraphUnion() - Method in class chemaxon.struc.RgMolecule: Gets a graph containing all the atoms and bonds.
getGraphUnion() - Method in class chemaxon.struc.RxnMolecule: Gets a graph containing all the atoms and bonds.
getGraphUnionAsSelection() - Method in class chemaxon.struc.Molecule: Gets a selection molecule containing all the atoms and bonds.
getGrinv(int[]) - Method in class chemaxon.struc.CGraph: Gets the graph invariants.
getGrinv() - Method in class chemaxon.struc.CGraph: Gets the graph invariants array.
getGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph: Gets the graph invariants.
getGrinv(int[], boolean) - Method in class chemaxon.struc.MoleculeGraph: Gets the graph invariants (canonical labels).
getGrinv(int[]) - Method in class chemaxon.struc.RgMolecule: Gets the graph invariants of the root structure.
getGrinv() - Method in class chemaxon.struc.RgMolecule: Gets the graph invariants of the root structure.
getGrinv(int[]) - Method in class chemaxon.struc.RxnMolecule: Gets the graph invariants for the graph union.
getGrinv() - Method in class chemaxon.struc.RxnMolecule: Gets the graph invariants for the graph union.
getGrinvCC() - Method in class chemaxon.struc.CGraph: Gets the graph invariant change count.
getHeteroRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the hetero ring count.
getHeteroaromaticRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the heteroaromatic ring count.
getHybridizationState() - Method in class chemaxon.struc.MolAtom: Gets the hybridization state.
getImageShowURL() - Method in class JMSketch
getImageSize(String) - Method in class chemaxon.struc.Molecule: Gets size information of an image created with the specified format string.
getImplicitHcount() - Method in class chemaxon.struc.MolAtom: Gets the number of implicit hydrogens attached.
getImplicitHcount() - Method in class chemaxon.struc.MoleculeGraph: Gets the total number of implicit hydrogens attached to the molecule.
getInputFormat() - Method in class chemaxon.struc.MDocument: Gets the input file format.
getInputFormat() - Method in class chemaxon.struc.Molecule: Gets the input file format.
getIsotope(int, int) - Static method in class chemaxon.struc.PeriodicSystem: Retrieves an isotope of the element
getIsotopeComposition() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the molecule isotope composition.
getIsotopeCount() - Static method in class chemaxon.struc.PeriodicSystem: Number of isotopes in the periodic system
getIsotopeCount(int) - Static method in class chemaxon.struc.PeriodicSystem: Number of isotopes of the element
getIsotopeFormula() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the molecule isotope formula.
getJtfFields(String) - Static method in class chemaxon.formats.MolInputStream: Gets fields delimited with {space} {tab} {;} {:} or {,}.
getL(int) - Method in class JMView: Gets a label.
getL(int) - Method in class MView: Gets a label.
getLargestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the largest ring size.
getLargestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the size of largest ring containing the specified atom.
getLegalAttachAtoms() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the legal attachment points.
getLength() - Method in class chemaxon.struc.MolBond: Gets the actual length of the bond.
getLicenseKey() - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the built-in license key for the given plugin class.
getLicenseKey() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the built-in license key for the given plugin class.
getLigand(int) - Method in class chemaxon.struc.CNode: Get the i-th ligand.
getLineColor() - Method in class chemaxon.struc.MObject: Gets the line color of the object.
getLineCount() - Method in class chemaxon.formats.MolInputStream: Gets the current line number.
getList() - Method in class chemaxon.struc.MolAtom: Gets the atom list.
getLocation() - Method in class chemaxon.struc.MPoint: Gets the point's location.
getLocation() - Method in class chemaxon.struc.MolAtom: Gets the coordinates.
getLocation(DPoint3) - Method in class chemaxon.struc.MolAtom: Gets the coordinates.
getLocation() - Method in class chemaxon.struc.MoleculeGraph: Gets the origin of the molecule.
getLock() - Method in class chemaxon.struc.CEdge: Gets lock object for synchronization.
getLock() - Method in class chemaxon.struc.CGraph: Gets the lock object for synchronization.
getLock() - Method in class chemaxon.struc.CNode: Get lock object for synchronization.
getLonePairCount(int) - Method in class chemaxon.struc.MoleculeGraph: Gets the number of lone pairs.
getM(int, String) - Method in class JMView: Gets the nth molecule in a text format.
getM(int, String) - Method in class MView: Gets the nth molecule in a text format.
getMObject() - Method in class chemaxon.marvin.sketch.MObjectSM
getMProperty(int, String) - Method in class JMView: Gets an RDfile/SDfile property.
getMProperty(int, String) - Method in class MView: Gets an RDfile/SDfile property.
getMPropertyCount(int) - Method in class JMView: Gets the number of RDfile/SDfile properties.
getMPropertyCount(int) - Method in class MView: Gets the number of RDfile/SDfile properties.
getMPropertyKey(int, int) - Method in class JMView: Gets an RDfile/SDfile property key.
getMPropertyKey(int, int) - Method in class MView: Gets an RDfile/SDfile property key.
getMainMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the molecule form with largest distribution.
getMainMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the molecule form with largest distribution.
getMainMoleculeGraph() - Method in class chemaxon.struc.MDocument: Gets the main molecule graph.
getMajorMicrospecies() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the major microspecies at the pH set in MajorMicrospeciesPlugin.setpH(double).
getMapCount() - Method in class chemaxon.marvin.modules.AutoMapper: Get number of solution maps found.
getMass() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the molecule mass.
getMass() - Method in class chemaxon.struc.MolAtom: Gets the atomic weight.
getMass() - Method in class chemaxon.struc.MoleculeGraph: Calculates the molecular weight of the molecule.
getMass(int) - Static method in class chemaxon.struc.PeriodicSystem: Atomic weight of the element based on the natural abundance of its isotopes
getMass(int, int) - Static method in class chemaxon.struc.PeriodicSystem: Atomic weight of the element
getMass() - Method in class chemaxon.struc.RgMolecule: Calculates the molecular weight of the molecule.
getMass() - Method in class chemaxon.struc.RxnMolecule: Calculates the molecular weight of the molecule.
getMassno() - Method in class chemaxon.struc.MolAtom: Gets the mass number.
getMaxRepetitions() - Method in class chemaxon.struc.MolAtom: Gets the maximum number of repetitions for a link node.
getMinRepetitions() - Method in class chemaxon.struc.MolAtom: Gets the minimum number of repetitions for a link node.
getModuleName(String) - Method in class chemaxon.marvin.plugin.CommandPlugger: Gets the module name for a command.
getMol(String) - Method in class JMSketch: Gets the molecule in a text format.
getMol(String) - Method in class MSketch: Gets the molecule in a text format.
getMol() - Method in class chemaxon.marvin.sketch.AtomSM: Gets a molecule instance corresponding to this template object.
getMol() - Method in class chemaxon.marvin.sketch.BondSM: Gets a molecule instance corresponding to this bond object.
getMol() - Method in class chemaxon.marvin.sketch.MObjectSM: Gets a molecule instance corresponding to the object stored.
getMol() - Method in class chemaxon.marvin.sketch.MoleculeSM: Gets the molecule reference stored in the object.
getMol() - Method in class chemaxon.marvin.sketch.SgroupSM: Gets a molecule instance containing the S-group's clone.
getMol() - Method in class chemaxon.marvin.sketch.SketchMode: Gets a molecule instance corresponding to the object stored.
getMolInputStream() - Method in interface chemaxon.marvin.util.MDocumentImportIface: Gets the molecule input stream.
getMolObject(int) - Method in class chemaxon.struc.graphics.MEFlow: Gets the electron source or sink.
getMolPolarizability() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the molecular polarizability value.
getMolProperty(String) - Method in class JMSketch: Gets an RDfile/SDfile property.
getMolProperty(String) - Method in class MSketch: Gets an RDfile/SDfile property.
getMolPropertyCount() - Method in class JMSketch: Gets the number of RDfile/SDfile properties.
getMolPropertyCount() - Method in class MSketch: Gets the number of RDfile/SDfile properties.
getMolPropertyKey(int) - Method in class JMSketch: Gets an RDfile/SDfile property key.
getMolPropertyKey(int) - Method in class MSketch: Gets an RDfile/SDfile property key.
getMolText() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the plugin molecule text to be displayed in the viewer.
getMolText() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the plugin molecule text to be displayed in the viewer.
getMolecule() - Method in class chemaxon.calculations.ElementalAnalyser: Retrieves the input molecule
getMolecule() - Method in class chemaxon.calculations.TopologyAnalyser: Retrieves the input molecule
getMoleculeGraph() - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets the stored molecule graph.
getMolfileVersion() - Method in class chemaxon.marvin.modules.MolExport: Gets the molfile version.
getMolfileVersion() - Method in class chemaxon.marvin.modules.MolImport: Gets the molfile version.
getMostFrequentNaturalIsotope(int) - Static method in class chemaxon.struc.PeriodicSystem: Returns the mass number of the most frequent natural isotope of the element
getMsAcceptorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the average acceptor counts over the microspecies distribution for different pH-s.
getMsCount() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the number of microspecies.
getMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the microspecies distribution array.
getMsDonorCounts() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the average donor counts over the microspecies distribution for different pH-s.
getMsMolecule(int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the microspecies molecule.
getMultiplier() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the multiplier.
getName() - Method in class chemaxon.struc.Molecule: Gets the molecule name.
getName(int) - Static method in class chemaxon.struc.PeriodicSystem: Name of the element
getName() - Method in class chemaxon.struc.RgMolecule: Gets the name of the root molecule.
getNode(int) - Method in class chemaxon.struc.CGraph: Gets a node.
getNode(int) - Method in class chemaxon.struc.RgMolecule: Gets a node of the root structure.
getNode(int) - Method in class chemaxon.struc.RxnMolecule: Gets a node.
getNode1() - Method in class chemaxon.struc.CEdge: Gets the first endpoint.
getNode2() - Method in class chemaxon.struc.CEdge: Gets the second endpoint.
getNodeCount() - Method in class chemaxon.struc.CGraph: Gets the number of nodes.
getNodeCount() - Method in class chemaxon.struc.RgMolecule: Gets the number of nodes in the root structure.
getNodeCount() - Method in class chemaxon.struc.RxnMolecule: Returns the number of nodes in the graph union.
getNodeVector() - Method in class chemaxon.struc.CGraph: Gets the nodes.
getNonAromrings() - Method in class chemaxon.struc.MoleculeGraph: Get alpihatic ring atom indexes.
getNonAromrings(int) - Method in class chemaxon.struc.MoleculeGraph: Get alpihatic ring atom indexes.
getNucleophilicEnergy(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
getNucleophilicOrder(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the nucleophilic order of an atom, -1 for no value.
getNumElectrons() - Method in class chemaxon.struc.graphics.MEFlow: Gets the number of electrons the arrow represents.
getObject(int) - Method in class chemaxon.struc.MDocument: Gets an object
getObjectContainingSelection() - Method in class chemaxon.struc.MDocument: Gets the object that contains the selection.
getObjectCount() - Method in class chemaxon.struc.MDocument: Gets the number of objects in this document.
getOptionSign() - Method in class chemaxon.marvin.util.MolExportModule: Gets the sign of an option.
getOptions() - Method in class chemaxon.marvin.util.MolExportModule: Returns the output options.
getOtherAtom(MolAtom) - Method in class chemaxon.struc.MolBond: Gets the other end of the bond.
getOtherNode(CNode) - Method in class chemaxon.struc.CEdge: Gets the other end of the edge.
getOutputClassName() - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the output provider class name for the command line interface.
getOutputClassName() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the output provider class name for the command line interface.
getParameterPanel() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the parameter panel.
getParameters() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the plugin parameters.
getParent() - Method in class chemaxon.struc.CEdge: Gets the parent graph.
getParent() - Method in class chemaxon.struc.CGraph: Gets the parent graph that contains this substructure.
getParent() - Method in class chemaxon.struc.CNode: Return the graph that contains this node.
getParentMolecule() - Method in class chemaxon.struc.Sgroup: Gets the parent molecule.
getParentSgroup() - Method in class chemaxon.struc.Sgroup: Gets the parent S-group.
getParity(int) - Method in class chemaxon.struc.MoleculeGraph: Computes the parity of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
getPiCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the pi charge of a specified atom.
getPiChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the pi charge density of an atom calculated with HMO, Double.NaN for no value.
getPiece(String) - Method in class JMSketch: Gets the current molecule piece in the specified format.
getPiece(String) - Method in class MSketch: Gets the current molecule piece in the specified format.
getPlugin() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the calculator plugin.
getPluginClassName() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the class name of the plugin.
getPoint(int) - Method in class chemaxon.struc.MObject: Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.MPoint: Gets the point.
getPoint(int) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the point.
getPoint(int) - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets a point of the object.
getPoint(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets a point of the line.
getPointCount() - Method in class chemaxon.struc.MObject: Gets the number of points.
getPointCount() - Method in class chemaxon.struc.MPoint: Gets the number of points.
getPointCount() - Method in class chemaxon.struc.graphics.MChemicalStruct: Gets the number of points (atoms).
getPointCount() - Method in class chemaxon.struc.graphics.MPolyline: Gets the number of points.
getPointRef(int) - Method in class chemaxon.struc.MObject: Gets a point of the object.
getPointRef(int) - Method in class chemaxon.struc.MPoint: Gets a point of the line.
getPointRef(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets a point of the line.
getPointRef(int) - Method in class chemaxon.struc.graphics.MRectangle: Gets an internal selectable point of the rectangle.
getPointRefCount() - Method in class chemaxon.struc.MObject: Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.MPoint: Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MPolyline: Gets the number of point references.
getPointRefCount() - Method in class chemaxon.struc.graphics.MRectangle: Gets the number of internal selectable point references.
getPointableAtomPairs(MoleculeGraph) - Method in class chemaxon.marvin.sketch.SketchMode: Gets the array of pointable atom pairs.
getPointableAtomPairs(MoleculeGraph) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Gets the array of pointable atom pairs.
getPointableAtoms(MoleculeGraph) - Method in class chemaxon.marvin.sketch.SketchMode: Gets the array of pointable atoms.
getPointableAtoms(MoleculeGraph) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Gets the array of pointable atoms.
getPointableBonds(MoleculeGraph) - Method in class chemaxon.marvin.sketch.SketchMode: Gets the array of pointable bonds.
getPointableBonds(MoleculeGraph) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Gets the array of pointable bonds.
getPointedAtomPairMinDstRatio2() - Method in class chemaxon.marvin.sketch.SketchMode: Cursor must be closer to the second atom of a highlighter pair than the distance of the two atoms times the returned value.
getPointedAtomPairMinDstRatio2() - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Cursor must be closer to the second atom of a highlighter pair than the distance of the two atoms times the returned value.
getPoints() - Method in class chemaxon.struc.MoleculeGraph: Gets an array containing the atom coordinates.
getPolarizability(int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the atom polarizability value.
getPolyline() - Method in class chemaxon.marvin.sketch.modules.LineSM
getPrincipalPolarizabilityComponents() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the principal components a(xx), a(yy), a(zz) of polarizability tensor (for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
getProduct(int) - Method in class chemaxon.struc.RxnMolecule: Gets a product.
getProductCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of products.
getProperty(String) - Method in class chemaxon.struc.Molecule: Gets an RDfile/SDfile property.
getProperty(String) - Method in class chemaxon.struc.RgMolecule: Gets an RDfile/SDfile property in the root structure.
getPropertyCount() - Method in class chemaxon.struc.Molecule: Gets the total number of RDfile/SDfile properties.
getPropertyCount() - Method in class chemaxon.struc.RgMolecule: Gets the total number of RDfile/SDfile properties.
getPropertyKey(int) - Method in class chemaxon.struc.Molecule: Gets an RDfile/SDfile property key.
getPropertyKey(int) - Method in class chemaxon.struc.RgMolecule: Gets an RDfile/SDfile property key.
getPropertyKeys() - Method in class chemaxon.struc.Molecule: Gets the keys for the RDfile/SDfile properties.
getPropertyKeys() - Method in class chemaxon.struc.RgMolecule: Gets the keys for the RDfile/SDfile properties.
getPropertyObject(String) - Method in class chemaxon.struc.Molecule: Gets an RDfile/SDfile property object.
getPropertyObject(String) - Method in class chemaxon.struc.RgMolecule: Gets an RDfile/SDfile property in the root structure.
getQProp(String) - Method in class chemaxon.struc.MolAtom: Gets a query property.
getQPropAsInt(String) - Method in class chemaxon.struc.MolAtom: Gets a query property as an integer.
getQueryAromaticity() - Method in class chemaxon.struc.MolAtom: Gets the aromatic/aliphatic query property.
getQueryLabel() - Method in class chemaxon.struc.MolAtom: Gets the string representation of the query atom
getQuerystr() - Method in class chemaxon.struc.MolAtom: Gets the query properties.
getQuerystr() - Method in class chemaxon.struc.MolBond: Gets the query properties.
getRadical() - Method in class chemaxon.struc.MolAtom: Gets the radical value.
getRadicalCount() - Method in class chemaxon.struc.MolAtom: Gets the number of free electrons.
getReactant(int) - Method in class chemaxon.struc.RxnMolecule: Gets a reactant.
getReactantCount() - Method in class chemaxon.struc.RxnMolecule: Gets the number of reactants.
getReaction(CGraph) - Static method in class chemaxon.struc.RxnMolecule: Returns the reaction represented by the given molecule if exists, otherwise null.
getReactionArrow() - Method in class chemaxon.struc.RxnMolecule: Gets a two-element array containing the endpoints of the reaction arrow.
getReactionArrowType() - Method in class chemaxon.struc.RxnMolecule: Gets the reaction arrow type.
getReactionArrowTypeName() - Method in class chemaxon.struc.RxnMolecule: Gets the reaction arrow type name.
getReactionStereo() - Method in class chemaxon.struc.MolAtom: Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
getRealBondCount() - Method in class chemaxon.struc.MolAtom: Gets the number of bonds connected to "real" atoms.
getRectangle() - Method in class chemaxon.marvin.sketch.modules.RectangleSM
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReferenceMolecule(Object, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the molecule to be used as reference image for the given result type and index.
getReflogDs() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the reference logD array.
getRefpHs() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the reference pH array.
getRefractivity() - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the refractivity value.
getRefractivityHIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the refractivity increment on the H atoms attached to a given atom.
getRefractivityIncrement(int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the refractivity increment for a given atom.
getRelativeNegativity() - Method in class chemaxon.struc.MolAtom: Check negativity compared to the neighbors.
getRepeatingUnitAtom(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets a paradigmatic repeating unit atom.
getRepeatingUnitAtomCount() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the number of atoms in the pararadigmatic repeating unit.
getResidueAtomId() - Method in class chemaxon.struc.MolAtom: Gets the residue atom identifier.
getResidueSeq() - Method in class chemaxon.struc.MolAtom: Gets the residue sequence number.
getResidueType() - Method in class chemaxon.struc.MolAtom: Gets the residue type.
getResourceBundle(String, String) - Static method in class chemaxon.marvin.plugin.CommandPlugger: Utility method to get a resource bundle.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the result item for the specified key and index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the atom count of a specific atom.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the majority microsepcies if pH is different from Double.NaN, otherwise returns the input molecule itself.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the result item for the specified type and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the result item for the specified type and index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the result item for the specified pH.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the result item for the specified key and index.
getResult(Object, int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the result item for the specified key and index.
getResult(Object, String) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the result item for the specified type ("acidic" or "basic") and the specified strongness index ("1" means the strongest value, "2" means the second strongest value, etc.) given in the argument string.
getResult(Object, int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the result item for the specified type and index.
getResult(Object, String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the result item for the specified argument string.
getResult(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the result item for the specified type and index.
getResult(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the result item for the specified argument string.
getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue): RED for acidic pKa, BLUE for basic pKa.
getResultAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the specified rsule molecule in SMILES format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the specified result in String format.
getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result in String format.
getResultAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result in String format for the first result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the number of result items for the given result type.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the number of result items: 1.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the number of result items for the given result key.
getResultCount(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the number of result items for the given result key.
getResultCount() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the number of result items for the first result type.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the calculation domain CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the calculation domain CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultDomain() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
getResultTypes() - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the result types (possible types: "sigma", "pi", "total").
getResultTypes() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.IonChargePlugin: Returns the result types (possible type: "charge").
getResultTypes() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the result types (possible types: "majority-ms").
getResultTypes() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Returns the result types (possible types: sigma, pi, total).
getResultTypes() - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the result types.
getResultTypes() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the result types (possible types: pKa, acidic, basic).
getResultTypes() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the result types.
getResultantImplicitHCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns sum of implicit H charge around a central atom
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsRGB(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the specified result in GUI-specific String format: A for acceptor, D for donor.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the specified results in String format.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the specified result with possible subresults (both pKa values instead of the most significant pKa) in String format.
getResultsAsString(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result with possible subresults.
getResultsAsString(int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the specified result with possible subresults.
getRgroup() - Method in class chemaxon.struc.MolAtom: Gets the R-group index.
getRgroupCount() - Method in class chemaxon.struc.RgMolecule: Gets the number of R-groups.
getRgroupId(int) - Method in class chemaxon.struc.RgMolecule: Gets the id of an R-group.
getRgroupMember(int, int) - Method in class chemaxon.struc.RgMolecule: Gets an R-group member.
getRgroupMemberCount(int) - Method in class chemaxon.struc.RgMolecule: Gets the number of R-group members.
getRingAtomCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the ring atom count.
getRingBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the ring bond count.
getRingCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the ring count.
getRlogic(int) - Method in class chemaxon.struc.RgMolecule: Gets R-logic flags.
getRlogicRange(int) - Method in class chemaxon.struc.RgMolecule: Gets R-logic occurence range.
getRoot() - Method in class chemaxon.struc.RgMolecule: Gets the root structure.
getRotatableBondCount() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the rotatable bond count.
getSSSR() - Method in class chemaxon.struc.CGraph: Gets the Smallest Set of Smallest Ring node indexes array.
getSSSRBondSet() - Method in class chemaxon.struc.MoleculeGraph: Get SSSR bond bitsets in integer array.
getScale() - Method in class JMSketch: Gets the magnification.
getScale() - Method in class MSketch: Gets the magnification.
getScale() - Method in class chemaxon.struc.CTransform3D: Gets the scale factor.
getSelectUtil() - Method in class chemaxon.marvin.sketch.RubberSM: Gets the selection utility.
getSelectUtil() - Method in class chemaxon.marvin.sketch.SelectSM: Gets the selection utility.
getSelectUtil() - Method in class chemaxon.marvin.sketch.SketchMode: Gets the selection utility.
getSelectedIndex() - Method in class JMView: Gets the index of the molecule that is selected by the user.
getSelectedIndex() - Method in class MView: Gets the index of the molecule that is selected by the user.
getSelectedString() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selected substring.
getSelectionEndPos() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's end position.
getSelectionStartPos() - Method in class chemaxon.struc.graphics.MTextBox: Gets the selection's start position.
getSetSeq() - Method in class chemaxon.struc.MolAtom: Gets the atom set sequence number.
getSetSeq() - Method in class chemaxon.struc.MolBond: Gets the bond set.
getSgroup(int) - Method in class chemaxon.struc.Molecule: Gets an S-group.
getSgroup() - Method in class chemaxon.struc.sgroup.SgroupAtom: Gets the S-group corresponding to this superatom.
getSgroupArray() - Method in class chemaxon.struc.Molecule: Gets the array of S-groups.
getSgroupCount() - Method in class chemaxon.struc.Molecule: Gets the number of S-groups.
getSgroupGraph() - Method in class chemaxon.struc.Sgroup: Gets the molecule graph.
getSgroupGraph() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the molecule graph as a selection.
getSgroupLigands() - Method in class chemaxon.struc.Molecule: Gets the S-group's ligands if the structure represents an S-group.
getSigmaCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the sigma charge of a specified atom.
getSimplifiedMolecule() - Method in class chemaxon.struc.Molecule: Gets the simplified molecule object.
getSimplifiedMolecule() - Method in class chemaxon.struc.RgMolecule: Gets the simplified molecule object.
getSingleMsDistribution(int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the microspecies distribution at the specified pH value set in pKaPlugin.setpH(double).
getSkip(int) - Method in class chemaxon.struc.graphics.MPolyline: Gets the distance of the (visible) head or tail from the corresponding line end point.
getSmallestRingSize() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the smallest ring size.
getSmallestRingSizeOfAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns the size of smallest ring containing the specified atom.
getSortedSgroups() - Method in class chemaxon.struc.Molecule: Gets the sorted S-groups in parent-child order.
getSortedValues(int, double[], int[]) - Method in class chemaxon.marvin.calculations.pKaPlugin: Calculates the least acidic pKa values in ascending order or the biggest basic pKa values in descending order.
getStartPoint() - Method in class chemaxon.marvin.sketch.modules.LineSM: Gets the start position of the currently drawn line.
getStartPosition() - Method in class chemaxon.struc.MDocument: Gets the starting position of this document in the input file.
getStartPosition() - Method in class chemaxon.struc.Molecule: Gets the starting position of this molecule in the input file.
getStereo1(CNode) - Method in class chemaxon.struc.MolBond: Gets wedge bond type relative to the specified chiral atom.
getStereo2(int, int, int, int) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(CNode, int, int, CNode) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, CNode, CNode) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, CNode, CNode, boolean) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans (Z/E) stereo information for the given bond.
getStereo2(MolBond, CNode, int, int, CNode) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereo2(MolBond, CNode, int, int, CNode, boolean) - Method in class chemaxon.struc.MoleculeGraph: Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
getStereoCare() - Method in class chemaxon.struc.MolAtom: Reports double bond stereo care information on the connected bonds.
getStereoGroupNumber() - Method in class chemaxon.struc.MolAtom: Gets the stereochemical group number.
getStereoGroupType() - Method in class chemaxon.struc.MolAtom: Gets the stereochemical group type.
getStructure(int, int) - Method in class chemaxon.struc.RxnMolecule: Gets a reactant, product or agent.
getStructureCount(int) - Method in class chemaxon.struc.RxnMolecule: Gets the number of reactants, products or agents.
getSubType() - Method in class chemaxon.struc.Sgroup: Gets polymer S-group subtype.
getSubscript() - Method in class chemaxon.struc.Sgroup: Gets the subscript for non-superatom S-groups.
getSubscript() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets the subscript.
getSuffix() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the plugin text suffix.
getSuffix() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the plugin text suffix.
getSuperAtom() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Gets the superatom.
getSuperscript() - Method in class chemaxon.struc.Sgroup: Gets the superscript for non-superatom S-groups.
getSymbol() - Method in class chemaxon.struc.MolAtom: Gets the element symbol.
getSymbol(int) - Static method in class chemaxon.struc.PeriodicSystem: Symbol of the element
getT(int) - Method in class JMView: Gets the value of a text field.
getT(int) - Method in class MView: Gets the value of a text field.
getTPSA() - Method in class chemaxon.marvin.calculations.TPSAPlugin: Returns the TPSA value.
getTabScale(int) - Method in class JMView: Gets the magnification for a molecule cell.
getTabScale(int) - Method in class MView: Gets the magnification for a molecule cell.
getTemporaryParameters() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns parameters from parameter panel without storing them in inner parameter structure.
getText() - Method in class chemaxon.struc.graphics.MTextBox: Gets the text stored.
getTextBox() - Method in class chemaxon.marvin.sketch.modules.TextBoxSM
getThickness() - Method in class chemaxon.struc.graphics.MPolyline: Gets the line thickness.
getThread() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the thread field.
getTitle() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns the title field.
getTotalCharge(int) - Method in class chemaxon.marvin.calculations.ChargePlugin: Returns the total charge of a specified atom.
getTotalChargeDensity(int) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
getTotalPiEnergy() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns the total pi energy of the input molecule.
getType() - Method in class chemaxon.marvin.sketch.BondSM
getType() - Method in class chemaxon.struc.MolBond: Gets the bond type.
getType() - Method in class chemaxon.struc.Sgroup: Gets S-group type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.calculations.logPPlugin: Returns a string representation of the given type.
getTypeString(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns a string representation of the given type.
getUserTypes() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the user defined result types.
getValence() - Method in class chemaxon.struc.MolAtom: Gets the valence.
getValenceProp() - Method in class chemaxon.struc.MolAtom: Gets the valence property.
getX() - Method in class chemaxon.struc.MPoint: Gets the x coordinate.
getX() - Method in class chemaxon.struc.MolAtom: Gets the X coordinate.
getX() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the x coordinate.
getXAxisLabel(Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the X axis label to be displayed in case of chart data.
getXAxisLabel(Object) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the X axis label to be displayed in case of chart data.
getXAxisLabel(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the X axis label to be displayed in case of chart data.
getXAxisLabel(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the X axis label to be displayed.
getXLabels() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the X label array (pH array as String[]).
getXLabels() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the X label array (pH array as String[]).
getXLabels() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the X label array (pH array as String[]).
getXLabels() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the X labels, X values formatted as strings.
getXState() - Method in class chemaxon.struc.Sgroup: Gets the expanded/contracted state.
getY() - Method in class chemaxon.struc.MPoint: Gets the y coordinate.
getY() - Method in class chemaxon.struc.MolAtom: Gets the Y coordinate.
getY() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the y coordinate.
getYAxisLabel(Object) - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the Y axis label to be displayed.
getYAxisLabel(Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the Y axis label to be displayed.
getYAxisLabel(Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns the Y axis label to be displayed.
getZ() - Method in class chemaxon.struc.MPoint: Gets the z coordinate.
getZ() - Method in class chemaxon.struc.MolAtom: Gets the Z coordinate.
getZ() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Gets the z coordinate.
getlogD() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the logD value for the pH specified in logDPlugin.setpH(double).
getlogDpI() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the logD value at pI.
getlogDs() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the logD array.
getlogPMicro() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the micro logP value.
getlogPNonionic() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the logP value for the non-ionic form.
getlogPTrue() - Method in class chemaxon.marvin.calculations.logPPlugin: Returns the most typical logP among logD at pI, micro logP and nonionic logP.
getpH() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns the pH where the majority microspecies should be taken.
getpHs() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns the pH array.
getpHs() - Method in class chemaxon.marvin.calculations.logDPlugin: Returns the pH array.
getpHs() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the pH array.
getpKa(int, int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns the pKa value for the given atom index and pKa type.
grinv - Variable in class chemaxon.struc.CGraph: Graph invariants.
grinvCC - Variable in class chemaxon.struc.CGraph: Graph invariant change count.

H

HBDAPlugin - class chemaxon.marvin.calculations.HBDAPlugin.: Plugin class for H bond acceptor/donor calculation.
HBDAPlugin() - Constructor for class chemaxon.marvin.calculations.HBDAPlugin: Constructor.
HEAD - Static variable in class chemaxon.struc.graphics.MPolyline: Arrow head.
HETERO - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the hetero any atom Q.
HS_S - Static variable in class chemaxon.struc.MolAtom: S hybridization state.
HS_SP - Static variable in class chemaxon.struc.MolAtom: SP hybridization state.
HS_SP2 - Static variable in class chemaxon.struc.MolAtom: SP2 hybridization state.
HS_SP3 - Static variable in class chemaxon.struc.MolAtom: SP3 hybridization state.
HS_UNKNOWN - Static variable in class chemaxon.struc.MolAtom: Unknown hybridization state.
HYDROGEN_VALENCE_ERROR_MSG - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
HuckelAnalysisPlugin - class chemaxon.marvin.calculations.HuckelAnalysisPlugin.: Plugin class for Huckel Analysis calculation.
HuckelAnalysisPlugin() - Constructor for class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Constructor.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
handlesMultiFragmentMolecules() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns true if the plugin handles multifragment molecules, false otherwise.
hasAromaticBond() - Method in class chemaxon.struc.MolAtom: Tests whether the atom has aromatic bond.
hasAtom(MolAtom) - Method in class chemaxon.struc.Sgroup: Is the specified atom an element of this group?
hasAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Is the specified atom an element of this group?
hasBackground() - Method in class chemaxon.struc.MObject: Can the object have a background?
hasBackground() - Method in class chemaxon.struc.graphics.MPolyline: A polyline has a background only if it is closed.
hasBackground() - Method in class chemaxon.struc.graphics.MTextBox: A text box has a background always.
hasBrackets() - Method in class chemaxon.struc.Sgroup: Checks if brackets should be painted or not.
hasBrackets() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Checks if brackets should be painted or not.
hasChart() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Returns true if plugin has chart.
hasColor() - Method in class chemaxon.struc.MObject: Can the object have a color (non-line and non-background)?
hasColor() - Method in class chemaxon.struc.graphics.MPolyline: A polyline does not have a non-line, non-background color.
hasColor() - Method in class chemaxon.struc.graphics.MTextBox: A text box has a text color.
hasExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph: Tests whether the molecule has implicit explici lone pair nodes.
hasFace() - Method in class chemaxon.struc.graphics.MPolyline: Is it 2 dimensional?
hasFace() - Method in class chemaxon.struc.graphics.MTextBox: Is it 2 dimensional?
hasImplicitH() - Method in class chemaxon.struc.MoleculeGraph: Indicates, whether the molecule has implicit hydrogen atoms.
hasLineColor() - Method in class chemaxon.struc.MObject: Can the object have a line color?
hasLineColor() - Method in class chemaxon.struc.graphics.MPolyline: A polyline have a line color always.
hasOutline() - Method in class chemaxon.struc.graphics.MPolyline: Does it have an outline?
hasQProps() - Method in class chemaxon.struc.MolAtom: Does it have query properties?
hasQueryBonds() - Method in class chemaxon.struc.MolAtom: Tests whether the atom has query bonds ("ANY" bonds).
hasSMARTSProps() - Method in class chemaxon.struc.MolAtom: Tests whether it is a SMARTS query atom.
hasSMARTSPropsExcluding(String) - Method in class chemaxon.struc.MolAtom: Tests whether it is a SMARTS query atom.
hasSelection() - Method in class chemaxon.struc.graphics.MChemicalStruct: Checks the existence of the selection.
hasSelection() - Method in class chemaxon.struc.graphics.MTextBox: Checks the existence of the selection.
hasValenceError() - Method in class chemaxon.struc.MolAtom: Determines if this atom has a valence error.
haveEqualProperties(CEdge) - Method in class chemaxon.struc.CEdge: Tests whether two bonds have the same properties.
haveEqualProperties(CNode) - Method in class chemaxon.struc.CNode: Checks if two nodes have the same properties.
haveEqualProperties(CNode) - Method in class chemaxon.struc.MolAtom: Tests if two atoms have the same properties.
haveEqualProperties(CEdge) - Method in class chemaxon.struc.MolBond: Tests whether two bonds have the same properties.
haveSimilarEdges(CNode) - Method in class chemaxon.struc.CNode: Checks if two nodes have similar edges.
heteroRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of heterocycles in the molecule (rings containing non-carbon atoms.
heteroaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of aromatic heterocycles in the molecule (aromatic rings containing non-carbon atoms.
highlight(MObject) - Method in class chemaxon.struc.MDocument: Highlight an object.
hydrogenize(boolean) - Method in class chemaxon.struc.MoleculeGraph: Implicit/explicit Hydrogen conversion.

I

INITIAL_CAPACITY - Static variable in class chemaxon.struc.CGraph: Initial capacity of the nodes and edges vectors.
ISOTOPE_H - Static variable in class chemaxon.struc.MolAtom: Include Hydrogen isotope(s).
IonChargePlugin - class chemaxon.marvin.calculations.IonChargePlugin.: Plugin class for charge calculation on ionized microspecies.
IonChargePlugin() - Constructor for class chemaxon.marvin.calculations.IonChargePlugin: Constructor.
implicitizeHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph: Removes explicit bound Hydrogens from the graph and converts them to implicit.
implicitizeHydrogens(int) - Method in class chemaxon.struc.RgMolecule: Removes explicit bound Hydrogens from the graph and converts them to implicit.
implicitizeHydrogens(int) - Method in class chemaxon.struc.RxnMolecule: Removes explicit bound Hydrogens from the graph and converts them to implicit.
incGrinvCC() - Method in class chemaxon.struc.CGraph: Increases the graph invariant change count and sets grinv to null.
indexOf(CNode) - Method in class chemaxon.struc.CGraph: Gets the index of the specified node.
indexOf(CEdge) - Method in class chemaxon.struc.CGraph: Gets the index of the specified edge.
indexOf(CEdge) - Method in class chemaxon.struc.CNode: Returns the index of the specified edge in this node.
indexOf(MObject) - Method in class chemaxon.struc.MDocument: Searches an object in the document.
indexOf(Sgroup) - Method in class chemaxon.struc.Molecule: Gets the array index of an S-group.
indexOf(CNode) - Method in class chemaxon.struc.RgMolecule: Gets the index of the specified node.
indexOf(CEdge) - Method in class chemaxon.struc.RgMolecule: Gets the index of the specified edge.
indexOf(CNode) - Method in class chemaxon.struc.RxnMolecule: Gets the index of the specified node in the graph union.
indexOf(CEdge) - Method in class chemaxon.struc.RxnMolecule: Gets the index of the specified edge in the graph union.
indexOf(MolAtom) - Method in class chemaxon.struc.Sgroup: Gets the atom index in the S-group graph.
init() - Method in class JMSketch: Initializes the applet.
init() - Method in class JMView: Initializes the applet.
init() - Method in class MSketch: Initializes the applet.
init() - Method in class MView: Initializes the applet.
init(String) - Method in class chemaxon.marvin.plugin.CommandPlugger: Initializes the plugger.
init(String) - Method in class chemaxon.marvin.sketch.MObjectPlugger: Initializes the plugger.
initLine(MPolyline) - Method in class chemaxon.marvin.sketch.modules.EFlowSM
initLine(MPolyline) - Method in class chemaxon.marvin.sketch.modules.LineSM
initMObject(MObject) - Method in class chemaxon.marvin.sketch.MObjectSM: Initializes sketcher object for the specified molecule editor.
initMObject(MObject) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Initializes a sketcher line object.
initMObject(MObject) - Method in class chemaxon.marvin.sketch.modules.LineSM: Initializes a sketcher line object.
initMObject(MObject) - Method in class chemaxon.marvin.sketch.modules.RectangleSM: Initializes a sketcher rectangle object.
initMObject(MObject) - Method in class chemaxon.marvin.sketch.modules.TextBoxSM: Initializes a sketcher text box object.
initMolImport(MolInputStream, String) - Method in class chemaxon.marvin.modules.MolImport: Start reading molecule(s) from MDL Mol, concatenated mol, or SDfile.
initMolImport(MolInputStream, String) - Method in interface chemaxon.marvin.util.MolImportIface: Initialization.
initSketchMode(MolEditor) - Method in class chemaxon.marvin.sketch.RubberSM: Initializes sketcher object for the specified molecule editor.
initSketchMode(MolEditor) - Method in class chemaxon.marvin.sketch.SketchMode: Initializes sketcher object for the specified molecule editor.
insertEdge(int, CEdge) - Method in class chemaxon.struc.CGraph: Inserts the edge at the specified index.
insertNode(int, CNode) - Method in class chemaxon.struc.CGraph: Inserts the node at the specified index.
insertNullEdges(int, int) - Method in class chemaxon.struc.CGraph: Insert nulls into the bond array.
insertNullEdges(int, int) - Method in class chemaxon.struc.RgMolecule: Insert nulls into the bond array.
insertNullNodes(int, int) - Method in class chemaxon.struc.CGraph: Insert nulls into the atom array.
insertNullNodes(int, int) - Method in class chemaxon.struc.RgMolecule: Insert nulls into the atom array.
insideLabel(double, double) - Method in class chemaxon.struc.MolAtom: Tests whether the specified point is inside the atom label.
invert() - Method in class chemaxon.struc.CTransform3D: Inverts the matrix.
ionChargeOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the ion charge.
isAbsStereo() - Method in class chemaxon.struc.MoleculeGraph: Gets the absolute stereoconfiguration flag.
isAliphaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if an atom is a member of an aromatic ring or not
isAromaticAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if an atom is a member of an aromatic ring or not
isAromaticAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns true if aromatic atom.
isArrow() - Method in class chemaxon.struc.MolBond: Tests if this edge represents a reaction arrow or not.
isArrow() - Method in class chemaxon.struc.graphics.MPolyline: Checks if it is an arrow.
isArrowEnd() - Method in class chemaxon.struc.MolAtom: Tests if this is an arrow endpoint.
isAtom() - Method in class chemaxon.struc.MoleculeGraph: Determines whether the structure represents only one atom and an arbitrary number of bonds.
isAtom() - Method in class chemaxon.struc.RgMolecule: Determines whether the structure represents only one atom and an arbitrary number of bonds.
isAtom() - Method in class chemaxon.struc.RxnMolecule: A reaction molecule cannot represent an atom.
isAtomSelected(int) - Method in class JMSketch: Returns true if atom is selected.
isAtomSelected(int) - Method in class MSketch: Returns true if atom is selected.
isAtomSetVisible(int) - Method in class JMView: Is the specified atom set visible?
isAtomSetVisible(int) - Method in class MView: Is the specified atom set visible?
isBond() - Method in class chemaxon.struc.MoleculeGraph: Determines whether the structure represents only one bond and zero or two atoms.
isBond() - Method in class chemaxon.struc.RgMolecule: Determines whether the structure represents only one bond and zero or two atoms.
isBond() - Method in class chemaxon.struc.RxnMolecule: A reaction molecule cannot represent a bond.
isBoundTo(CNode) - Method in class chemaxon.struc.CNode: Checks if this CNode is connected to another one or not.
isBracketVisible() - Method in class chemaxon.struc.Sgroup: Tests whether the bracket is visible.
isBracketVisible() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Tests whether the bracket is visible.
isBracketVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Tests whether the bracket is visible.
isChainAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if an atom a ring bond or a chain bond
isChainAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns true if chain atom.
isChainBond(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if a bond is a ring bond or a chain bond
isChildOf(MObject) - Method in class chemaxon.struc.MObject: Is this object a children of another one?
isChildOf(MObject) - Method in class chemaxon.struc.MPoint: Is this object a children of another one?
isContracted() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Is this S-group contracted?
isContracted() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Is this S-group contracted?
isCurrentJoinHighlighted() - Method in class chemaxon.marvin.sketch.AtomSM: Join points are highlighted always except when the pointed object is a bond.
isCurrentJoinHighlighted() - Method in class chemaxon.marvin.sketch.SketchMode: Are the current join points highlighted?
isEmpty() - Method in class JMSketch: Returns true sketcher canvas is empty.
isEmpty(int) - Method in class JMView: Returns true if molecule cell is empty.
isEmpty() - Method in class MSketch: Returns true sketcher canvas is empty.
isEmpty(int) - Method in class MView: Returns true if molecule cell is empty.
isEmpty() - Method in class chemaxon.struc.CGraph: Ask if the graph is empty or not.
isEmpty() - Method in class chemaxon.struc.MDocument
isEmpty() - Method in class chemaxon.struc.MObject: An object may become empty if all the children are removed.
isEmpty() - Method in class chemaxon.struc.RgMolecule: Ask if the molecule is empty or not.
isEmpty() - Method in class chemaxon.struc.RxnMolecule: Ask if the reaction is empty or not.
isEmpty() - Method in class chemaxon.struc.Sgroup: Is it an empty S-group?
isEmpty() - Method in class chemaxon.struc.graphics.MChemicalStruct: A chemical structure object is empty if the molecule graph is empty.
isEmpty() - Method in class chemaxon.struc.graphics.MPolyline: A polyline becomes empty if it has less than 2 points.
isEmpty() - Method in class chemaxon.struc.graphics.MTextBox: A text box is empty if the string contains only whitespace.
isExpanded() - Method in interface chemaxon.struc.sgroup.Expandable: Is this S-group expanded?
isExpanded() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Is this S-group expanded?
isExpanded() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Is this S-group expanded?
isGUIContracted() - Method in class chemaxon.struc.Molecule: Checks if the molecule has a GUI-contracted S-group or not.
isHighlighted(MObject) - Method in class chemaxon.struc.MDocument: Is the specified object currently highlighted?
isImplicitHcountImportant(MolAtom) - Static method in class chemaxon.marvin.util.MolExportModule: Checks whether the number of implicit hydrogens is important information for an atom or not.
isImplicitizableH(int) - Method in class chemaxon.struc.MolAtom: Tests whether the hydrogen atom is implicitizable or not.
isIncompleteReaction() - Method in class chemaxon.struc.RgMolecule: Check whether the reaction is incomplete or not.
isIncompleteReaction() - Method in class chemaxon.struc.RxnMolecule: Check whether the reaction is incomplete or not.
isInternalSelectable() - Method in class chemaxon.struc.MObject: Is it a selection only internal object?
isInternalSelectable() - Method in class chemaxon.struc.MPoint: Is it a selection only internal object?
isLegalAttachment(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Checks if the specified atom is attached to a legal attachment point.
isLicensed() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns true if the plugin is licensed (has a license key).
isLinkNode() - Method in class chemaxon.struc.MolAtom: The atom is a link node if the maximum number of repetitions is nonzero.
isMajorMs() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Returns true if major microspecies required, ie, if pH is different from Double.NaN.
isMajorMs() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns true if major microspecies required, false otherwise.
isMajorityMsCalculation() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns true if majority microspecies calculation takes place, ie, if pH is different formDouble.NaN.
isMappable() - Method in class chemaxon.struc.MolAtom: Is it a mappable atom?
isMsCalc() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns true if microspecies calculation.
isMsCalc() - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns true if microspecies calculation.
isMsCalc() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns true if microspecies calculation.
isMultiChiral - Variable in class chemaxon.struc.MoleculeGraph: true if there are at least two chiral centres
isMultiChiral() - Method in class chemaxon.struc.MoleculeGraph: Returns the multiple chirality flag.
isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Returns whether the result can be ignored.
isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.calculations.pKaPlugin: Returns whether the result can be ignored.
isNegligibleResult(Object, int, Object) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns whether the result can be ignored.
isNobleGas() - Method in class chemaxon.struc.MolAtom: Is it a noble gas?
isPseudo() - Method in class chemaxon.struc.MolAtom: Tests whether if the atom is a pseudo atom.
isQProp() - Method in class chemaxon.struc.MolAtom: Tests whether this object represents a query property.
isQuery() - Method in class chemaxon.struc.MolAtom: Tests whether it is a query atom.
isQuery() - Method in class chemaxon.struc.MolBond: Is it a query bond?
isReaction() - Method in class chemaxon.struc.Molecule: Checks if the structure represents a reaction or not.
isReaction() - Method in class chemaxon.struc.RgMolecule: Checks if the structure represents a reaction or not.
isReaction() - Method in class chemaxon.struc.RxnMolecule: Checks if the structure represents a reaction or not.
isRealNodeParent() - Method in class chemaxon.struc.CGraph: Can it be a real node parent?
isRealNodeParent() - Method in class chemaxon.struc.RgMolecule: R-group molecule objects cannot be real node parents.
isRealNodeParent() - Method in class chemaxon.struc.RxnMolecule: Reaction molecules cannot be real node parents.
isRealNodeParent() - Method in class chemaxon.struc.SelectionMolecule: Selection molecules are not real node parents.
isRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Checks if the specified atom object is in the paradigmatic repeating unit or not.
isRgrouped(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin: Returns true if molecule with R-groups.
isRingAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if an atom a ring bond or a chain bond
isRingAtom(int) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Returns true if ring atom.
isRingBond(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if a bond is a ring bond or a chain bond
isRingBond(int) - Method in class chemaxon.struc.MoleculeGraph: Is this bond in ring?
isRotatableBond(int) - Method in class chemaxon.calculations.TopologyAnalyser: Determine if a bond is a rotatable or not
isRubber() - Method in class chemaxon.marvin.sketch.RubberSM: Is it a rubber object?
isRubber() - Method in class chemaxon.marvin.sketch.SketchMode: Is it a rubber object?
isSameParityClass(int, int, int, int, int, int, int, int) - Static method in class chemaxon.struc.MolAtom: Calculates if chirality centers in the structure and the query belong to the same parity class.
isSelectableNow() - Method in class chemaxon.struc.MObject: Is the object selectable now?
isSelected(int, int) - Method in class JMView: Is the specified atom selected?
isSelected(int, int) - Method in class MView: Is the specified atom selected?
isSelected() - Method in class chemaxon.struc.MObject: Is the object selected?
isSelected() - Method in class chemaxon.struc.MolAtom: Tests whether this atom is selected.
isSetVisible(int) - Method in class JMView: Deprecated. as of Marvin 3.3, replaced by isAtomSetVisible
isSetVisible(int) - Method in class MView: Deprecated. as of Marvin 3.3, replaced by isAtomSetVisible
isSgroup() - Method in class chemaxon.struc.Molecule: Checks if the structure represents an S-group or not.
isSimilarTo(CGraph) - Method in class chemaxon.struc.CGraph: Checks if the graph is similar to another graph.
isSimilarTo(CGraph) - Method in class chemaxon.struc.MoleculeGraph: Checks if the graph is similar to another graph.
isTemporaryObjectPaintingNeeded() - Method in class chemaxon.marvin.sketch.SketchMode: Checks if temporary object painting is needed.
isTemporaryObjectPaintingNeeded() - Method in class chemaxon.marvin.sketch.modules.LineSM: Checks if temporary line object painting is needed.
isTemporaryObjectPaintingNeeded() - Method in class chemaxon.marvin.sketch.modules.RectangleSM: Checks if temporary rectangle object painting is needed.
isTerminalAtom() - Method in class chemaxon.struc.MolAtom: Determines whether it is a terminal atom or not.
isThicknessSet() - Method in class chemaxon.struc.graphics.MPolyline: Checks if the line thickness is set.
isTransformable() - Method in class chemaxon.struc.MObject: Is it a transformable object?
isTransformable() - Method in class chemaxon.struc.graphics.MAtomSetPoint: Is it a transformable object?
isValidEndPoint(MPoint) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Checks if the specified end point is valid for this line type.
isValidEndPoint(MPoint) - Method in class chemaxon.marvin.sketch.modules.LineSM: Checks if the specified end point is valid for this line type.
isValidStartPoint(MPoint) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Checks if the specified starting point is valid for this line type.
isValidStartPoint(MPoint) - Method in class chemaxon.marvin.sketch.modules.LineSM: Checks if the specified starting point is valid for this line type.
isVisible() - Method in class chemaxon.struc.Sgroup: Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.
isotopeComposition(int) - Method in class chemaxon.calculations.ElementalAnalyser: Gets the molecular composition (w/w%).
isotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser: Gets the molecular formula (isotopes are separated).
isotopeType(int, int) - Static method in class chemaxon.struc.MolAtom: Gets the type of an isotope.

J

JMSketch - class JMSketch.: Swing version of the MarvinSketch Applet.
JMSketch() - Constructor for class JMSketch
JMView - class JMView.: Swing version of the MarvinView Applet.
JMView() - Constructor for class JMView
join(Thread) - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Joins the runner thread and sets the next thread.

L

LIST - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the inclusive atom list.
LONELY_H - Static variable in class chemaxon.struc.MolAtom: Include lonely Hydrogen atom(s).
LP - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the lonely pair.
LineSM - class chemaxon.marvin.sketch.modules.LineSM.: Line drawing mode.
LineSM() - Constructor for class chemaxon.marvin.sketch.modules.LineSM: Creates a line sketch mode object.
LineSM(LineSM) - Constructor for class chemaxon.marvin.sketch.modules.LineSM: Copy constructor.
LineSM(MPolyline, int) - Constructor for class chemaxon.marvin.sketch.modules.LineSM: Creates a line sketch mode object.
largestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the size of the largest ring in the molecule (SSSR based).
largestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the size of the largest ring an atom is a member of (SSSR based).
loadMarvinModule(String) - Static method in class chemaxon.marvin.util.MolExportModule: Loads a molecule export module for the specified format.
logDPlugin - class chemaxon.marvin.calculations.logDPlugin.: Plugin class for logD calculation.
logDPlugin() - Constructor for class chemaxon.marvin.calculations.logDPlugin: Constructor.
logPPlugin - class chemaxon.marvin.calculations.logPPlugin.: Plugin class for logP calculation.
logPPlugin() - Constructor for class chemaxon.marvin.calculations.logPPlugin: Constructor.

M

MAPPED_H - Static variable in class chemaxon.struc.MolAtom: Mapped Hydrogen atom(s).
MAtomSetPoint - class chemaxon.struc.graphics.MAtomSetPoint.: Point fixed to the location of one or more atoms.
MAtomSetPoint() - Constructor for class chemaxon.struc.graphics.MAtomSetPoint: Contructs an empty point object.
MAtomSetPoint(MolAtom[]) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint: Contructs a point object.
MAtomSetPoint(MAtomSetPoint) - Constructor for class chemaxon.struc.graphics.MAtomSetPoint: Copy constructor.
MChemicalStruct - class chemaxon.struc.graphics.MChemicalStruct.: Molecule graph object.
MChemicalStruct(MoleculeGraph) - Constructor for class chemaxon.struc.graphics.MChemicalStruct: Contructs a molecule graph object.
MChemicalStruct(MChemicalStruct) - Constructor for class chemaxon.struc.graphics.MChemicalStruct: Copy constructor.
MDL_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable: MDL like multiple group expansion flag.
MDocument - class chemaxon.struc.MDocument.: Marvin document.
MDocument(MoleculeGraph) - Constructor for class chemaxon.struc.MDocument: Creates a document for the specified molecule graph.
MDocument(MDocument) - Constructor for class chemaxon.struc.MDocument: Copy constructor.
MDocument(MDocument, boolean) - Constructor for class chemaxon.struc.MDocument: Copy constructor.
MDocumentImportIface - interface chemaxon.marvin.util.MDocumentImportIface.: Marvin document reader interface.
MEFlow - class chemaxon.struc.graphics.MEFlow.: Electron flow arrow.
MEFlow() - Constructor for class chemaxon.struc.graphics.MEFlow: Contructs an empty electron flow arrow.
MEFlow(int) - Constructor for class chemaxon.struc.graphics.MEFlow: Contructs an empty electron flow arrow.
MEFlow(MPoint, MPoint, int) - Constructor for class chemaxon.struc.graphics.MEFlow: Contructs an electron flow arrow with the specified endpoints.
MEFlow(MEFlow) - Constructor for class chemaxon.struc.graphics.MEFlow: Copy constructor.
MOLECULE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Calculation domain type: calculation refers to the molecule.
MObject - class chemaxon.struc.MObject.: Paintable object.
MObject(Color, Color, Color) - Constructor for class chemaxon.struc.MObject: Contructs a paintable object with the specified color.
MObject(MObject) - Constructor for class chemaxon.struc.MObject: Copy constructor.
MObjectPlugger - class chemaxon.marvin.sketch.MObjectPlugger.: Graphics object plug-in handler.
MObjectPlugger() - Constructor for class chemaxon.marvin.sketch.MObjectPlugger
MObjectSM - class chemaxon.marvin.sketch.MObjectSM.: Graphics object placement mode.
MObjectSM() - Constructor for class chemaxon.marvin.sketch.MObjectSM: Constructs a sketch object for the specified document object.
MObjectSM(MolEditor, MObject) - Constructor for class chemaxon.marvin.sketch.MObjectSM: Constructs a sketch object for the specified document object.
MObjectSM(MolEditor) - Constructor for class chemaxon.marvin.sketch.MObjectSM: Constructs a sketch object.
MObjectSM(MObjectSM) - Constructor for class chemaxon.marvin.sketch.MObjectSM: Copy constructor.
MPoint - class chemaxon.struc.MPoint.: Point object.
MPoint(double, double, double) - Constructor for class chemaxon.struc.MPoint: Contructs a point object.
MPoint(DPoint3) - Constructor for class chemaxon.struc.MPoint: Constructs a point object.
MPoint(MPoint) - Constructor for class chemaxon.struc.MPoint: Copy constructor.
MPolyline - class chemaxon.struc.graphics.MPolyline.: Polyline object.
MPolyline() - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs an empty line.
MPolyline(MPoint, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs a line with the specified endpoints.
MPolyline(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs a line with the specified endpoints.
MPolyline(boolean, Color, Color) - Constructor for class chemaxon.struc.graphics.MPolyline: Creates a closed polyline.
MPolyline(MPolyline) - Constructor for class chemaxon.struc.graphics.MPolyline: Copy constructor.
MPolyline(MPolyline, MPoint) - Constructor for class chemaxon.struc.graphics.MPolyline: Contructs a polyline from the specified starting polyline and endpoint.
MRectangle - class chemaxon.struc.graphics.MRectangle.: Rectangle object.
MRectangle() - Constructor for class chemaxon.struc.graphics.MRectangle: Contructs a rectangle.
MRectangle(MPoint, MPoint, Color, Color) - Constructor for class chemaxon.struc.graphics.MRectangle: Contructs a rectangle with the specified corner points.
MRectangle(MRectangle) - Constructor for class chemaxon.struc.graphics.MRectangle: Copy constructor.
MSelectionDocument - class chemaxon.struc.MSelectionDocument.: Selection document.
MSelectionDocument(SelectionMolecule) - Constructor for class chemaxon.struc.MSelectionDocument: Creates a document for the specified molecule graph.
MSelectionDocument(MSelectionDocument) - Constructor for class chemaxon.struc.MSelectionDocument: Copy constructor.
MSketch - class MSketch.: AWT version of the MarvinSketch Applet.
MSketch() - Constructor for class MSketch
MTextBox - class chemaxon.struc.graphics.MTextBox.: Text box object.
MTextBox() - Constructor for class chemaxon.struc.graphics.MTextBox: Contructs an empty text box.
MTextBox(MTextBox) - Constructor for class chemaxon.struc.graphics.MTextBox: Copy constructor.
MView - class MView.: AWT version of the MarvinView Applet.
MView() - Constructor for class MView
MajorMicrospeciesPlugin - class chemaxon.marvin.calculations.MajorMicrospeciesPlugin.: Plugin class that calculates the major microspecies on a given pH.
MajorMicrospeciesPlugin() - Constructor for class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Constructor.
MdlCompressor - class chemaxon.formats.MdlCompressor.: Molfile compression.
MdlCompressor(InputStream, OutputStream, int) - Constructor for class chemaxon.formats.MdlCompressor: Create a(n un)compressor for the specified input and output streams.
MolAtom - class chemaxon.struc.MolAtom.: Atom object and the properties of the elements.
MolAtom(int, double, double, double) - Constructor for class chemaxon.struc.MolAtom: Construct an atom.
MolAtom(double, double) - Constructor for class chemaxon.struc.MolAtom: Construct a carbon atom at the specified location.
MolAtom(int) - Constructor for class chemaxon.struc.MolAtom: Construct an atom of the specified type at the origin.
MolBond - class chemaxon.struc.MolBond.: Chemical bond.
MolBond(MolAtom, MolAtom, int) - Constructor for class chemaxon.struc.MolBond: Construct a bond between two atoms.
MolBond(MolBond) - Constructor for class chemaxon.struc.MolBond: Copy constructor.
MolBond(MolAtom, MolAtom) - Constructor for class chemaxon.struc.MolBond: Construct a single bond between two atoms.
MolExport - class chemaxon.marvin.modules.MolExport.: Exports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (ChemAxon) compressed molfile.
MolExport() - Constructor for class chemaxon.marvin.modules.MolExport: Constructor.
MolExportException - exception chemaxon.marvin.util.MolExportException.: Molecule export exception.
MolExportException(String) - Constructor for class chemaxon.marvin.util.MolExportException: Creates a molecule export exception with the specified message.
MolExportModule - class chemaxon.marvin.util.MolExportModule.: Abstract base class of molecule export modules.
MolExportModule() - Constructor for class chemaxon.marvin.util.MolExportModule
MolImport - class chemaxon.marvin.modules.MolImport.: Imports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (ChemAxon) compressed molfile.
MolImport() - Constructor for class chemaxon.marvin.modules.MolImport
MolImportIface - interface chemaxon.marvin.util.MolImportIface.: Molecule reader interface.
MolInputStream - class chemaxon.formats.MolInputStream.: Molecule input stream that has the ability to determine the input file format.
MolInputStream(InputStream, String) - Constructor for class chemaxon.formats.MolInputStream: Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(InputStream) - Constructor for class chemaxon.formats.MolInputStream: Create a molecule input stream from an ordinary one, and determine the format.
Molecule - class chemaxon.struc.Molecule.: Molecule class.
Molecule(Molecule, int, int) - Constructor for class chemaxon.struc.Molecule: Construct a molecule or fragment with the specified number of atoms and bonds.
Molecule(Molecule, MolAtom) - Constructor for class chemaxon.struc.Molecule: Construct a graph consisting of a single vertex (atom).
Molecule(Molecule, MolBond) - Constructor for class chemaxon.struc.Molecule: Construct a graph consisting of a single edge (bond).
Molecule(Molecule) - Constructor for class chemaxon.struc.Molecule: Construct a molecule or fragment.
Molecule() - Constructor for class chemaxon.struc.Molecule: Construct a molecule.
MoleculeGraph - class chemaxon.struc.MoleculeGraph.: A graph consisting of MolAtom vertices and MolBond edges.
MoleculeGraph(MoleculeGraph, int, int) - Constructor for class chemaxon.struc.MoleculeGraph: Construct a molecule or fragment with the specified number of atoms and bonds.
MoleculeGraph(MoleculeGraph) - Constructor for class chemaxon.struc.MoleculeGraph: Construct a molecule or fragment.
MoleculeGraph() - Constructor for class chemaxon.struc.MoleculeGraph: Construct a molecule.
MoleculeSM - class chemaxon.marvin.sketch.MoleculeSM.: Molecule placement mode.
MoleculeSM(MolEditor, Molecule) - Constructor for class chemaxon.marvin.sketch.MoleculeSM: Constructs a sketcher molecule object.
MoleculeSM(MoleculeSM) - Constructor for class chemaxon.marvin.sketch.MoleculeSM: Copy constructor.
MoleculeSM(MolEditor) - Constructor for class chemaxon.marvin.sketch.MoleculeSM: Constructs a sketcher molecule object.
MultipleSgroup - class chemaxon.struc.sgroup.MultipleSgroup.: Multiple S-group.
MultipleSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup: Constructs a multiple S-group.
MultipleSgroup(MultipleSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup: Copy constructor.
m00 - Variable in class chemaxon.struc.CTransform3D: The m00 element of the matrix.
m01 - Variable in class chemaxon.struc.CTransform3D: The m01 element of the matrix.
m02 - Variable in class chemaxon.struc.CTransform3D: The m02 element of the matrix.
m03 - Variable in class chemaxon.struc.CTransform3D: The m03 element of the matrix.
m10 - Variable in class chemaxon.struc.CTransform3D: The m10 element of the matrix.
m11 - Variable in class chemaxon.struc.CTransform3D: The m11 element of the matrix.
m12 - Variable in class chemaxon.struc.CTransform3D: The m12 element of the matrix.
m13 - Variable in class chemaxon.struc.CTransform3D: The m13 element of the matrix.
m20 - Variable in class chemaxon.struc.CTransform3D: The m20 element of the matrix.
m21 - Variable in class chemaxon.struc.CTransform3D: The m21 element of the matrix.
m22 - Variable in class chemaxon.struc.CTransform3D: The m22 element of the matrix.
m23 - Variable in class chemaxon.struc.CTransform3D: The m23 element of the matrix.
m30 - Variable in class chemaxon.struc.CTransform3D: The m30 element of the matrix.
m31 - Variable in class chemaxon.struc.CTransform3D: The m31 element of the matrix.
m32 - Variable in class chemaxon.struc.CTransform3D: The m32 element of the matrix.
m33 - Variable in class chemaxon.struc.CTransform3D: The m33 element of the matrix.
main(String[]) - Static method in class chemaxon.formats.MdlCompressor: Main program.
mainMChemicalStruct - Variable in class chemaxon.struc.MDocument
makeBondMol(int) - Static method in class chemaxon.marvin.sketch.BondSM
makeColor(String) - Static method in class chemaxon.struc.MObject
makeColorString(Color) - Static method in class chemaxon.struc.MObject: Makes a string from a Color object.
makeItSimilar(CGraph) - Method in class chemaxon.struc.CGraph: Empty method.
makeItSimilar(CGraph) - Method in class chemaxon.struc.Molecule: Copies some properties of this molecule to the other one specified as argument.
makeItSimilar(CGraph) - Method in class chemaxon.struc.MoleculeGraph: Copies some properties of this molecule to the other one specified as argument.
map(RxnMolecule) - Method in class chemaxon.marvin.modules.AutoMapper: Convenience function that unifies setReaction() and setMap() in one method.
mapReaction(RxnMolecule) - Static method in class chemaxon.marvin.modules.AutoMapper: Convenience function that unifies setReaction() and setMap() in one method.
mass() - Method in class chemaxon.calculations.ElementalAnalyser: Calculates the molecular weight of the molecule.
mergeNodes(CNode, CNode) - Method in class chemaxon.struc.CGraph: Merges edges of a node with another node, then adds the node to the molecule.
mergeNodes(CNode, CNode) - Method in class chemaxon.struc.Molecule: Merges bonds of an atom with another atom, then add the atom to the molecule.
mergeNodes(CNode, CNode) - Method in class chemaxon.struc.MoleculeGraph: Merges edges of a node with another node, then adds the node to the molecule.
mergeNodes(CNode, CNode) - Method in class chemaxon.struc.RgMolecule: Merges bonds of an atom with another atom, then add the atom to the molecule.
mergeNodes(CNode, CNode) - Method in class chemaxon.struc.RxnMolecule: Merges bonds of an atom with another atom, then add the atom to the molecule.
modfunc(Object) - Method in class chemaxon.marvin.modules.AutoMapper: Method to be implemented in modules.
molecule - Variable in class chemaxon.marvin.sketch.MoleculeSM
mouseClicked(MouseEvent) - Method in class JMSketch: Does nothing.
mouseEntered(MouseEvent) - Method in class JMSketch: Does nothing.
mouseExited(MouseEvent) - Method in class JMSketch: Does nothing.
mousePressed(MouseEvent) - Method in class JMSketch: Does nothing.
mouseReleased(MouseEvent) - Method in class JMSketch: Handles the viewer button press events.
mouseUp(Event, int, int) - Method in class MSketch: Handle the viewer button press events
moveMainMoleculeGraphToFront() - Method in class chemaxon.struc.MDocument: Move the main molecule graph to the top of stack.
moveObject(MObject, int) - Method in class chemaxon.struc.MDocument: Move an object to another place in the stack.
moveTo(DPoint3) - Method in class chemaxon.marvin.sketch.AtomSM
moveTo(DPoint3) - Method in class chemaxon.marvin.sketch.BondSM
moveTo(DPoint3) - Method in class chemaxon.marvin.sketch.MoleculeSM
moveTo(DPoint3, Molecule) - Static method in class chemaxon.marvin.sketch.MoleculeSM
moveTo(DPoint3) - Method in class chemaxon.marvin.sketch.SketchMode
moveTo(DPoint3) - Method in class chemaxon.struc.MoleculeGraph: Move the molecule.
mul(CTransform3D) - Method in class chemaxon.struc.CTransform3D: Multiplies by another matrix.

N

NAN - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Double constant for Double.NaN.
NONRECURSIVE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable: Recursive expansion of child groups.
NOTLIST - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the exclusive atom list.
nFrags - Variable in class chemaxon.struc.CGraph: Number of disconnected fragments.
nGrinv - Variable in class chemaxon.struc.CGraph: Number of different graph invariants.
nameOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the name of the specified element.
naturalWeightOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the natural weight of the element.
nedges - Variable in class chemaxon.struc.CNode: Number of edges.
negOxOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the negative oxidation number.
newInstance() - Method in class chemaxon.struc.CGraph: Creates a new CGraph object.
newInstance() - Method in class chemaxon.struc.Molecule: Creates a new Molecule object.
newInstance() - Method in class chemaxon.struc.MoleculeGraph: Creates a new MoleculeGraph object.
newInstance() - Method in class chemaxon.struc.RgMolecule: Creates a new RgMolecule object.
newInstance() - Method in class chemaxon.struc.RxnMolecule: Creates a new RxnMolecule object.
newInstance() - Method in class chemaxon.struc.sgroup.MultipleSgroup: Gets a new MultipleSgroup instance.
newRectangle() - Method in class chemaxon.marvin.sketch.modules.RectangleSM
node1 - Variable in class chemaxon.struc.CEdge: Node at one end of the edge.
node2 - Variable in class chemaxon.struc.CEdge: Node at the other end of the edge.
nodeCount - Variable in class chemaxon.struc.CGraph: The number of nodes.
nodes - Variable in class chemaxon.struc.CGraph: The nodes (atoms).
numOf(String) - Static method in class chemaxon.struc.MolAtom: Gets the atomic number of an element.
numoxstatesOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the number of oxidation states for the specified element.

O

ORPHANS - Static variable in class chemaxon.marvin.modules.AutoMapper: missing orphan/widow atom maps are added
objectContainingSelection - Variable in class chemaxon.struc.MDocument
objects - Variable in class chemaxon.struc.MDocument
open(String) - Method in class chemaxon.marvin.modules.MolExport: Open the exporter stream.
open(String) - Method in class chemaxon.marvin.util.MolExportModule: Open the exporter stream.
orix - Variable in class chemaxon.struc.MoleculeGraph: Origin x.
oriy - Variable in class chemaxon.struc.MoleculeGraph: Origin y.
oriz - Variable in class chemaxon.struc.MoleculeGraph: Origin z.
overridesAtMerge(CEdge) - Method in class chemaxon.struc.CEdge: Checks if this bond should override another one when two structures are merged.
overridesAtMerge(CEdge) - Method in class chemaxon.struc.MolBond: Checks if this bond should override another one when two structures are merged.
oxstateOf(int, int) - Static method in class chemaxon.struc.MolAtom: Gets the oxidation states.

P

PAINT_ANTIALIAS - Static variable in class chemaxon.struc.MObject: Antialias flag.
PAINT_FOCUSED - Static variable in class chemaxon.struc.MObject: Input focus on the component (MTextBox).
PARITY_EITHER - Static variable in interface chemaxon.struc.StereoConstants: Odd or even parity.
PARITY_EVEN - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of even parity.
PARITY_MASK - Static variable in interface chemaxon.struc.StereoConstants: Parity mask in flags.
PARITY_ODD - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of odd parity.
PARITY_UNSPEC - Static variable in interface chemaxon.struc.StereoConstants: Chiral atom of unspecified parity.
POLYLINE - Static variable in class chemaxon.marvin.sketch.modules.LineSM
PRODUCTS - Static variable in class chemaxon.struc.RxnMolecule: "Product" structure type.
PSEUDO - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of a pseudoatom.
PeriodicSystem - class chemaxon.struc.PeriodicSystem.: Periodic System of the Elements.
PeriodicSystem() - Constructor for class chemaxon.struc.PeriodicSystem
PluginException - exception chemaxon.marvin.plugin.PluginException.: Exception thrown in case of plugin processing or calculation errors.
PluginException() - Constructor for class chemaxon.marvin.plugin.PluginException: Default constructor.
PluginException(String) - Constructor for class chemaxon.marvin.plugin.PluginException: Constructor with message.
PluginException(Exception) - Constructor for class chemaxon.marvin.plugin.PluginException: Constructor with wrapped exception.
PluginException(String, int) - Constructor for class chemaxon.marvin.plugin.PluginException: Constructor with message.
PluginException(Exception, int) - Constructor for class chemaxon.marvin.plugin.PluginException: Constructor with wrapped exception.
PolarizabilityPlugin - class chemaxon.marvin.calculations.PolarizabilityPlugin.: Plugin class for atom polarizability calculation.
PolarizabilityPlugin() - Constructor for class chemaxon.marvin.calculations.PolarizabilityPlugin: Constructor.
PolylineSM - class chemaxon.marvin.sketch.modules.PolylineSM.: Polyline drawing mode.
PolylineSM() - Constructor for class chemaxon.marvin.sketch.modules.PolylineSM
PolylineSM(PolylineSM) - Constructor for class chemaxon.marvin.sketch.modules.PolylineSM: Copy constructor.
pKaPlugin - class chemaxon.marvin.calculations.pKaPlugin.: Plugin class for macro/micro pKa calculation.
pKaPlugin() - Constructor for class chemaxon.marvin.calculations.pKaPlugin: Constructor.
pack() - Method in class chemaxon.struc.CGraph: Reduce memory usage.
pack() - Method in class chemaxon.struc.CNode: Reduce memory usage.
paint(Graphics, CTransform3D, int, Color, Color, Color) - Method in class chemaxon.struc.MObject: Paints the object.
paint(Graphics, CTransform3D, int, Color, Color, Color) - Method in class chemaxon.struc.MPoint: Paints the object.
paint(Graphics, CTransform3D, int, Color, Color, Color) - Method in class chemaxon.struc.graphics.MPolyline: Paints the object.
paint(Graphics, CTransform3D, int, Color, Color, Color) - Method in class chemaxon.struc.graphics.MTextBox: Paints the object.
paintTemporaryObject(Graphics) - Method in class chemaxon.marvin.sketch.SketchMode: Paints a temporary object before creating the persistent one.
paintTemporaryObject(Graphics) - Method in class chemaxon.marvin.sketch.modules.LineSM: Paints a temporary line object before creating the persistent one.
paintTemporaryObject(Graphics) - Method in class chemaxon.marvin.sketch.modules.RectangleSM: Paints a temporary rectangle object before creating the persistent one.
paintTemps1(Graphics) - Method in class chemaxon.marvin.sketch.RubberSM
paintTemps1(Graphics) - Method in class chemaxon.marvin.sketch.SelectSM
paintTemps1(Graphics) - Method in class chemaxon.marvin.sketch.SketchMode
parentGraph - Variable in class chemaxon.struc.CGraph: The structure that contains this graph as a substructure.
paritySign(int, int, int, int) - Static method in class chemaxon.struc.MolAtom: Calculates the sign of the parity for the specified indexes.
parseOption(String, int) - Method in class chemaxon.marvin.modules.MolExport: Parses the bond length (b###) option.
parseOption(String, int) - Method in class chemaxon.marvin.util.MolExportModule: Parses the following option in the option string.
pointerDrag(int) - Method in class chemaxon.marvin.sketch.AtomSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.BondSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.MObjectSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.MoleculeSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.RubberSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.SelectSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.SgroupSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.SketchMode
pointerDrag(int) - Method in class chemaxon.marvin.sketch.modules.EFlowSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.modules.LineSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.modules.RectangleSM
pointerDrag(int) - Method in class chemaxon.marvin.sketch.modules.TextBoxSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.AtomSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.BondSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.MObjectSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.MoleculeSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.RubberSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.SelectSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.SgroupSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.SketchMode
pointerMove(int) - Method in class chemaxon.marvin.sketch.modules.EFlowSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.modules.LineSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.modules.RectangleSM
pointerMove(int) - Method in class chemaxon.marvin.sketch.modules.TextBoxSM
posOxOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the smallest positive oxidation number.
postImage(String, String) - Method in class JMSketch: Posts image to CGI script.
postInit(boolean) - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader
preconvert(Molecule) - Method in class chemaxon.marvin.util.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(Molecule, boolean) - Method in class chemaxon.marvin.util.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(Molecule, boolean, int) - Method in class chemaxon.marvin.util.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
preconvert(MoleculeGraph, boolean, int) - Method in class chemaxon.marvin.util.MolExportModule: Optionally performs aromatization or addition of explicit Hydrogens atoms.
preload() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Loads the calculator plugin.
prepareMolPaint() - Method in class chemaxon.marvin.sketch.RubberSM
prepareMolPaint() - Method in class chemaxon.marvin.sketch.SelectSM
prepareMolPaint() - Method in class chemaxon.marvin.sketch.SketchMode
printStackTrace(PrintStream) - Method in class chemaxon.marvin.plugin.PluginException: Prints the stack trace together with the stack trace of the wrapped exception.
printStackTrace(PrintWriter) - Method in class chemaxon.marvin.plugin.PluginException: Prints the stack trace together with the stack trace of the wrapped exception.
putBackLine() - Method in class chemaxon.formats.MolInputStream: Puts back the last line into the stream.

Q

qpropCheck() - Method in class chemaxon.struc.MolAtom: Query property checking.
qpropCheck(Vector) - Method in class chemaxon.struc.MoleculeGraph: Check for query property errors.

R

RAD1 - Static variable in class chemaxon.struc.MolAtom: Monovalent radical center.
RAD2 - Static variable in class chemaxon.struc.MolAtom: Divalent radical center.
RAD2_SINGLET - Static variable in class chemaxon.struc.MolAtom: Divalent radical center with singlet electronic configuration.
RAD2_TRIPLET - Static variable in class chemaxon.struc.MolAtom: Divalent radical center with triplet electronic configuration.
RAD3 - Static variable in class chemaxon.struc.MolAtom: Trivalent radical center.
RADICAL_H - Static variable in class chemaxon.struc.MolAtom: Include radical Hydrogen atom(s).
RAD_COUNT_MASK - Static variable in class chemaxon.struc.MolAtom: Radical's free electron count bits in flags.
RAD_MASK - Static variable in class chemaxon.struc.MolAtom: Radical value bits in flags.
RAD_OFF - Static variable in class chemaxon.struc.MolAtom: Radical value offset in flags.
REACTANTS - Static variable in class chemaxon.struc.RxnMolecule: "Reactant" structure type.
RED - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Constant storing the red rgb value (the acidic pKa result color).
RESSEQ_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum residue sequence number is currently 8191.
RESTYPE_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum residue type is currently 63.
REVERSIBLE_EXPAND - Static variable in interface chemaxon.struc.sgroup.Expandable: Reversible expansion or contraction.
RGROUP - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of the Rgroup query "atom".
RGROUPED - Static variable in class chemaxon.struc.RxnMolecule: Add R-groups to component structure.
RGROUP_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum R-group index.
RG_ID2_MASK - Static variable in class chemaxon.struc.RgMolecule: Mask of the other R-group's id in R-logic.
RG_ID2_OFF - Static variable in class chemaxon.struc.RgMolecule: Offset of the other R-group's id in R-logic.
RG_ID_MASK - Static variable in class chemaxon.struc.RgMolecule: R-group id mask in R-logic.
RG_RESTH - Static variable in class chemaxon.struc.RgMolecule: The RestH flag in R-logic.
RMCLEANUP_ALL - Static variable in class chemaxon.struc.CGraph: Perform all clean-up methods when removing a node or an edge.
RMCLEANUP_EDGES - Static variable in class chemaxon.struc.CGraph: When removing a node or an edge, also remove the edge(s) from the node object(s).
RMCLEANUP_NONE - Static variable in class chemaxon.struc.CGraph: Do not perform any clean-up methods when removing a node or an edge.
RMCLEANUP_STEREO - Static variable in class chemaxon.struc.MoleculeGraph: When removing a H atom, keep stereo information unchanged.
RXNSTEREO_INVERSION - Static variable in class chemaxon.struc.MolAtom: The stereo configuration of the atom is inverted during the reaction.
RXNSTEREO_NONE - Static variable in class chemaxon.struc.MolAtom: The stereo configuration of the atom is not considered during the reaction.
RXNSTEREO_RETENTION - Static variable in class chemaxon.struc.MolAtom: The stereo configuration of the atom is retained during the reaction.
RectangleSM - class chemaxon.marvin.sketch.modules.RectangleSM.: Rectangle drawing mode.
RectangleSM() - Constructor for class chemaxon.marvin.sketch.modules.RectangleSM: Constructs a sketcher rectangle object.
RectangleSM(RectangleSM) - Constructor for class chemaxon.marvin.sketch.modules.RectangleSM: Copy constructor.
RectangleSM(MRectangle) - Constructor for class chemaxon.marvin.sketch.modules.RectangleSM: Constructs a sketcher rectangle object.
RefractivityPlugin - class chemaxon.marvin.calculations.RefractivityPlugin.: Plugin class for refractivity calculation.
RefractivityPlugin() - Constructor for class chemaxon.marvin.calculations.RefractivityPlugin: Constructor.
RgMolecule - class chemaxon.struc.RgMolecule.: A molecule or reaction containing R-groups.
RgMolecule() - Constructor for class chemaxon.struc.RgMolecule: Creates an RgMolecule.
RubberSM - class chemaxon.marvin.sketch.RubberSM.: Deletion mode.
RubberSM() - Constructor for class chemaxon.marvin.sketch.RubberSM: Creates a sketcher eraser object.
RubberSM(MolEditor) - Constructor for class chemaxon.marvin.sketch.RubberSM: Creates a sketcher eraser object for the specified molecule editor.
RubberSM(RubberSM) - Constructor for class chemaxon.marvin.sketch.RubberSM: Copy constructor.
RxnMolecule - class chemaxon.struc.RxnMolecule.: Reaction.
RxnMolecule() - Constructor for class chemaxon.struc.RxnMolecule: Create a reaction.
read() - Method in class chemaxon.formats.MolInputStream: Reads a character.
read(byte[], int, int) - Method in class chemaxon.formats.MolInputStream: Reads a byte array.
read16doubles(ObjectInput) - Method in class chemaxon.struc.CTransform3D: Reads the 4x4 matrix components as double precision floating point numbers.
read16floats(ObjectInput) - Method in class chemaxon.struc.CTransform3D: Reads the 4x4 matrix components as single precision floating point numbers.
readDocument(MDocument) - Method in interface chemaxon.marvin.util.MDocumentImportIface: Reads the next document.
readExternal(ObjectInput) - Method in class chemaxon.struc.CTransform3D: Deserializes a transformation matrix.
readExternal(ObjectInput) - Method in class chemaxon.struc.DPoint3: Deserializes a 3D point.
readLine() - Method in class chemaxon.formats.MolInputStream: Reads a line.
readMol(Molecule) - Method in class chemaxon.marvin.modules.MolImport: Reads a molecule.
readMol(Molecule) - Method in interface chemaxon.marvin.util.MolImportIface: Reads the next molecule.
rebuildStructures() - Method in class chemaxon.struc.RxnMolecule: For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow.
rebuildStructures(DPoint3[], int) - Method in class chemaxon.struc.RxnMolecule: Sets the reaction arrow.
recalcReactionArrow() - Method in class chemaxon.struc.RxnMolecule: Recalculates the reaction arrow, forced recalculation.
regenCtabs() - Method in class chemaxon.struc.CGraph: Regenerates connection table and edge table.
regenCtabs() - Method in class chemaxon.struc.SelectionMolecule: Regenerates connection table and edge table.
regenEdges() - Method in class chemaxon.struc.CGraph: Regenerates the edge vector: remove its elements, then put the edge objects from the nodes into it.
regenEdges() - Method in class chemaxon.struc.RgMolecule: Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
regenEdges() - Method in class chemaxon.struc.RxnMolecule: Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
reloadParameters() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Reloads parameters to parameter panel.
removeAll() - Method in class chemaxon.struc.CGraph: Removes all the nodes and edges.
removeAll() - Method in class chemaxon.struc.Molecule: Removes all the nodes and edges.
removeAll() - Method in class chemaxon.struc.RgMolecule: Remove all the atoms and bonds from the root structure, and from all the R-groups.
removeAll() - Method in class chemaxon.struc.RxnMolecule: Remove all the atoms and bonds from the root structure, and from all the R-groups.
removeAllEdges() - Method in class chemaxon.struc.CGraph: Removes all edges.
removeAllEdges() - Method in class chemaxon.struc.CNode: Remove all edges.
removeAllEdges() - Method in class chemaxon.struc.Molecule: Removes all edges.
removeAllEdges() - Method in class chemaxon.struc.RgMolecule: Remove all bonds from the root structure, and from all the R-groups.
removeAllEdges() - Method in class chemaxon.struc.RxnMolecule: Removes all bonds from the reactants, products and agents.
removeAllEdges() - Method in class chemaxon.struc.sgroup.SgroupAtom: Remove all edges.
removeAllSgroups() - Method in class chemaxon.struc.Molecule: Removes all S-groups.
removeAtom(MolAtom) - Method in class chemaxon.struc.MDocument: Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
removeAtom(MolAtom) - Method in class chemaxon.struc.Sgroup: Removes an atom and its bonds from the S-group.
removeAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Removes an atom from the S-group.
removeAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes an atom from the S-group.
removeBond(MolBond) - Method in class chemaxon.struc.Sgroup: Removes a bond from the S-group.
removeBond(MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Removes a bond from the S-group.
removeChild(MObject) - Method in class chemaxon.struc.MObject: Removes a child object.
removeChild(MObject) - Method in class chemaxon.struc.graphics.MPolyline
removeChild(MObject) - Method in class chemaxon.struc.graphics.MRectangle
removeEdge(CEdge) - Method in class chemaxon.struc.CGraph: Removes an edge by reference.
removeEdge(int) - Method in class chemaxon.struc.CGraph: Removes an edge from the graph.
removeEdge(CEdge, int) - Method in class chemaxon.struc.CGraph: Removes an edge by reference.
removeEdge(int, int) - Method in class chemaxon.struc.CGraph: Removes an edge from the graph.
removeEdge(int) - Method in class chemaxon.struc.CNode: Remove an edge.
removeEdge(CEdge) - Method in class chemaxon.struc.CNode: Remove an edge by reference.
removeEdge(int) - Method in class chemaxon.struc.MolAtom: Removes a bond.
removeEdge(CEdge, int) - Method in class chemaxon.struc.Molecule: Removes an edge by reference.
removeEdge(int, int) - Method in class chemaxon.struc.Molecule: Removes an edge.
removeEdge(CEdge, int) - Method in class chemaxon.struc.RgMolecule: Remove a bond from the root structure, and from all the R-groups.
removeEdge(int, int) - Method in class chemaxon.struc.RgMolecule: Remove a bond from the root structure.
removeEdge(CEdge, int) - Method in class chemaxon.struc.RxnMolecule: Removes a bond from the reactants, products or agents.
removeEdge(int, int) - Method in class chemaxon.struc.RxnMolecule: Removes an edge from a reactant, agent or product.
removeEdge(CEdge) - Method in class chemaxon.struc.SelectionMolecule: Removes an edge by reference.
removeEdge(int) - Method in class chemaxon.struc.SelectionMolecule: Removes an edge from the graph.
removeEdge(int) - Method in class chemaxon.struc.sgroup.SgroupAtom: Removes a bond.
removeEdges() - Method in class chemaxon.struc.Sgroup: Removes the edge references.
removeExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph: Removes explicit lone pairs.
removeGroupedAtom(MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.struc.Sgroup: Removes an atom from the molecule and remove its specified bonds.
removeNode(CNode) - Method in class chemaxon.struc.CGraph: Removes a node and its edges.
removeNode(int) - Method in class chemaxon.struc.CGraph: Removes a node and its edges from the graph.
removeNode(CNode, int) - Method in class chemaxon.struc.CGraph: Removes a node and its edges with extra clean-up options.
removeNode(int, int) - Method in class chemaxon.struc.CGraph: Removes a node and its edges with extra clean-up options.
removeNode(CNode, int) - Method in class chemaxon.struc.Molecule: Removes a node and its edges.
removeNode(int, int) - Method in class chemaxon.struc.Molecule: Remove a node and its edges.
removeNode(CNode, int) - Method in class chemaxon.struc.MoleculeGraph: Removes a node and its edges with extra options.
removeNode(int, int) - Method in class chemaxon.struc.MoleculeGraph: Removes a node and its edges with extra options.
removeNode(CNode, int) - Method in class chemaxon.struc.RgMolecule: Removes an atom and its bonds from the root structure and from all the R-groups.
removeNode(int, int) - Method in class chemaxon.struc.RgMolecule: Removes an atom and its bonds from the root structure.
removeNode(CNode, int) - Method in class chemaxon.struc.RxnMolecule: Removes an atom from the reactants, products or agents.
removeNode(int, int) - Method in class chemaxon.struc.RxnMolecule: Removes an atom from the reactants, products or agents.
removeNode(CNode) - Method in class chemaxon.struc.SelectionMolecule: Removes a node and its edges.
removeNode(int) - Method in class chemaxon.struc.SelectionMolecule: Removes a node and its edges from the graph.
removeNodeFromGraphs(CNode) - Method in class chemaxon.struc.MDocument: Removes the specified node from all molecule graphs.
removeNotify() - Method in class chemaxon.struc.MObject: Called when the object is removed from a document.
removeObject(MObject) - Method in class chemaxon.struc.MDocument: Removes an object from the document.
removeObject(int) - Method in class chemaxon.struc.MDocument: Removes an object from the document.
removeObject(MObject) - Method in class chemaxon.struc.MSelectionDocument: Removes an object from the document.
removeObject(int) - Method in class chemaxon.struc.MSelectionDocument: Removes an object from the document.
removeSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule: Removes S-groups from this object and its parent.
removeStructure(int, int) - Method in class chemaxon.struc.RxnMolecule: Removes a reactant, product or agent.
removeWhitespace(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin: Removes whitespace characters from the given string.
reparentSgroups(Molecule) - Method in class chemaxon.struc.Molecule: Change parents of all S-groups in this molecule.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.MObject: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.Sgroup: Replace an existing atom by a new one in this S-group and its parent (recursively).
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.graphics.MPolyline: Replaces a contained atom with another one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Replace an existing atom by a new one.
replaceAtom(MolAtom, MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Replace an existing atom by a new one.
reset() - Method in class chemaxon.formats.MolInputStream: Repositions this stream to the position at the time the mark method was last called on this input stream.
reset() - Method in class chemaxon.marvin.sketch.RubberSM
reset() - Method in class chemaxon.marvin.sketch.SelectSM
reset() - Method in class chemaxon.marvin.sketch.SketchMode
reset() - Method in class chemaxon.marvin.sketch.modules.LineSM: Clears the start point and the click point.
reset() - Method in class chemaxon.marvin.sketch.modules.RectangleSM: Clears the start point and the click point.
resetCtab() - Method in class chemaxon.struc.CGraph: An operation performed that changed the connection table and the graph invariants.
resetGrinvInParents() - Method in class chemaxon.struc.CGraph: Graph invariants must be recalculated for this graph and all parent graphs.
residueSymbolOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the name of a residue.
residueSymbolOf(int) - Static method in class chemaxon.struc.Molecule: Gets the name of a residue.
residueTypeOf(String) - Static method in class chemaxon.struc.MolAtom: Gets the residue identifier for a residue name.
residueTypeOf(String) - Static method in class chemaxon.struc.Molecule: Gets the residue identifier for a residue name.
restoreCache(int) - Method in class chemaxon.struc.CGraph: Restores caches like connection table, bond table, etc.
restoreCache(int) - Method in class chemaxon.struc.MoleculeGraph: Restores caches like connection table, bond table, etc.
reuseAtom(int, int) - Method in class chemaxon.struc.Molecule: Reuse an atom or create a new one.
reuseAtom(int, int) - Method in class chemaxon.struc.RgMolecule: Reuse an atom or create a new one.
rgroupIdOf(CNode) - Method in class chemaxon.struc.RgMolecule: Finds the ID of the R-group (the number in R#) that contains the specified atom.
rgroupIndexOf(CNode) - Method in class chemaxon.struc.RgMolecule: Finds the index of the R-group (the number in R#) that contains the specified atom.
ringAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of ring atoms in the molecule.
ringBondCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of ring bonds in the molecule.
ringCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of rings (SSSR smallest set of smallest rings) in the molecule.
ringCount(int) - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
ringCountOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
rotatableBondCount() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the number of rotatable bonds in the molecule.
run() - Method in class JMSketch: Runs the thread that handles JavaScript calls.
run() - Method in class JMView: Runs the thread that handles JavaScript calls.
run() - Method in class MSketch: Runs the thread that handles JavaScript calls.
run() - Method in class MView: Runs the thread that handles JavaScript calls.
run() - Method in class chemaxon.marvin.calculations.ChargePlugin: Runs the charge calculation.
run() - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Runs the tool.
run() - Method in class chemaxon.marvin.calculations.HBDAPlugin: Runs the charge calculation.
run() - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Runs the Huckel analysis calculation.
run() - Method in class chemaxon.marvin.calculations.IonChargePlugin: Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH.
run() - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Does nothing, the input molecule is already standardized and set to the majority microsepcies.
run() - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Runs the charge calculation.
run() - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Runs the logP calculation.
run() - Method in class chemaxon.marvin.calculations.TPSAPlugin: Runs the logP calculation.
run() - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Runs the tool.
run() - Method in class chemaxon.marvin.calculations.logDPlugin: Runs the logD calculation.
run() - Method in class chemaxon.marvin.calculations.logPPlugin: Runs the logP calculation.
run() - Method in class chemaxon.marvin.calculations.pKaPlugin: Runs the macro pKa calculation.
run() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Runs the tool.

S

SCN_EITHER_UNKNOWN - Static variable in class chemaxon.struc.Sgroup: Either unknown S-group connectivity.
SCN_HEAD_TO_HEAD - Static variable in class chemaxon.struc.Sgroup: Head-to-head S-group connectivity.
SCN_HEAD_TO_TAIL - Static variable in class chemaxon.struc.Sgroup: Head-to-tail S-group connectivity.
SDF - Static variable in class chemaxon.formats.MdlCompressor
SETSEQ_MAX - Static variable in class chemaxon.struc.MolAtom: Maximum atom set sequence number is currently 63.
SETSEQ_MAX - Static variable in class chemaxon.struc.MolBond: Maximum bond set sequence number.
SETSEQ_OFF - Static variable in class chemaxon.struc.MolBond: Bond set sequence number offset in flags.
SGROUP - Static variable in class chemaxon.struc.MolAtom: "Atomic number" of an Sgroup.
SINGLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond: Single or aromatic query bond type.
SINGLE_OR_DOUBLE - Static variable in class chemaxon.struc.MolBond: Single or double query bond type.
SMARTS_H_DAYLIGHT_COMP_MODE - Static variable in class chemaxon.struc.MolAtom: Option flag to express daylight-type smarts atom parsing of H.
SMARTS_H_MARVIN_COMP_MODE - Static variable in class chemaxon.struc.MolAtom: Option flag to express marvin-pre-3.5-type smarts atom parsing of H.
SORT_CHILD_PARENT - Static variable in class chemaxon.struc.Sgroup: Parent-child sort order.
SORT_PARENT_CHILD - Static variable in class chemaxon.struc.Sgroup: Parent-child sort order.
SST_ALTERNATING - Static variable in class chemaxon.struc.Sgroup: Alternating polymer S-group subtype.
SST_BLOCK - Static variable in class chemaxon.struc.Sgroup: Block polymer S-group subtype.
SST_RANDOM - Static variable in class chemaxon.struc.Sgroup: Random polymer S-group subtype.
STEREO1_MASK - Static variable in class chemaxon.struc.MolBond: Single bond stereo mask.
STEREO2_CARE - Static variable in class chemaxon.struc.MolBond: Cis/trans info of this bond is taken care of during the SSS process if this flag is set - used only for query bonds.
STEREO_MASK - Static variable in class chemaxon.struc.MolBond: Single and double bond stereo mask.
STGRP_ABS - Static variable in interface chemaxon.struc.StereoConstants: Absolute stereo group type.
STGRP_AND - Static variable in interface chemaxon.struc.StereoConstants: AND stereo group type.
STGRP_NONE - Static variable in interface chemaxon.struc.StereoConstants: Empty stereo group type setting.
STGRP_OR - Static variable in interface chemaxon.struc.StereoConstants: OR stereo group type.
ST_ANY - Static variable in class chemaxon.struc.Sgroup: Any polymer S-group type.
ST_COPOLYMER - Static variable in class chemaxon.struc.Sgroup: Copolymer S-group type.
ST_CROSSLINK - Static variable in class chemaxon.struc.Sgroup: Crosslink S-group type.
ST_DATA - Static variable in class chemaxon.struc.Sgroup: Data S-group type.
ST_FORMULATION - Static variable in class chemaxon.struc.Sgroup: Formulation S-group type.
ST_GENERIC - Static variable in class chemaxon.struc.Sgroup: Generic S-group type.
ST_MER - Static variable in class chemaxon.struc.Sgroup: Mer S-group type.
ST_MIXTURE - Static variable in class chemaxon.struc.Sgroup: Mixture S-group type.
ST_MODIFICATION - Static variable in class chemaxon.struc.Sgroup: Modification S-group type.
ST_MONOMER - Static variable in class chemaxon.struc.Sgroup: Monomer S-group type.
ST_MULTIPLE - Static variable in class chemaxon.struc.Sgroup: Multiple group S-group type.
ST_SRU - Static variable in class chemaxon.struc.Sgroup: SRU S-group type.
ST_SUPERATOM - Static variable in class chemaxon.struc.Sgroup: Superatom S-group type.
SUBRESULT - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin: Calculation domain type: subresult to be displayed in a separate text area.
SelectSM - class chemaxon.marvin.sketch.SelectSM.: Selection mode.
SelectSM(MolEditor) - Constructor for class chemaxon.marvin.sketch.SelectSM: Creates a sketcher selector object for the specified molecule editor.
SelectSM(SelectSM) - Constructor for class chemaxon.marvin.sketch.SelectSM: Copy constructor.
SelectionMolecule - class chemaxon.struc.SelectionMolecule.: A selection object derived from Molecule's ancestor.
SelectionMolecule() - Constructor for class chemaxon.struc.SelectionMolecule
Sgroup - class chemaxon.struc.Sgroup.: S-group.
Sgroup(Molecule, int) - Constructor for class chemaxon.struc.Sgroup: Creates an S-group with the specified parent and type.
Sgroup(Molecule, int, int) - Constructor for class chemaxon.struc.Sgroup: Creates an S-group with the specified parent and type.
Sgroup(Sgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.Sgroup: Copy constructor.
SgroupAtom - class chemaxon.struc.sgroup.SgroupAtom.: S-group.
SgroupAtom(SuperatomSgroup) - Constructor for class chemaxon.struc.sgroup.SgroupAtom: Constructs a superatom for a superatom type S-group.
SgroupSM - class chemaxon.marvin.sketch.SgroupSM.: S-group mode.
SgroupSM(MolEditor, Sgroup) - Constructor for class chemaxon.marvin.sketch.SgroupSM: Creates a sketcher S-group object.
SgroupSM(SgroupSM) - Constructor for class chemaxon.marvin.sketch.SgroupSM: Copy constructor.
SketchMode - class chemaxon.marvin.sketch.SketchMode.: Abstract base class of sketching modes.
SketchMode() - Constructor for class chemaxon.marvin.sketch.SketchMode: Creates a sketcher object for the specified molecule editor.
SketchMode(MolEditor) - Constructor for class chemaxon.marvin.sketch.SketchMode: Creates a sketcher object for the specified molecule editor.
SketchMode(SketchMode) - Constructor for class chemaxon.marvin.sketch.SketchMode: Copy constructor.
StereoConstants - interface chemaxon.struc.StereoConstants.: Constants for atom parity and double bond stereo.
SuperatomSgroup - class chemaxon.struc.sgroup.SuperatomSgroup.: Superatom S-group.
SuperatomSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup: Constructs a superatom S-group in expanded state.
SuperatomSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup: Constructs a superatom S-group.
SuperatomSgroup(SuperatomSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup: Copy constructor.
saveCache(int) - Method in class chemaxon.struc.CGraph: Saves caches like connection table, bond table, etc.
saveCache(int) - Method in class chemaxon.struc.MoleculeGraph: Saves caches like connection table, bond table, etc.
saveLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Saves licenses in license file.
selectAllAtoms(int, boolean) - Method in class JMView: Select or unselect all atoms in the specified molecule.
selectAllAtoms(int, boolean) - Method in class MView: Select or unselect all atoms in the specified molecule.
selectAllObjects(boolean) - Method in class chemaxon.struc.MDocument: Selects or unselects all objects.
selectAtom(int, int, boolean) - Method in class JMView: Select or unselect an atom in the specified molecule.
selectAtom(int, int, boolean) - Method in class MView: Select or unselect an atom in the specified molecule.
set(CTransform3D) - Method in class chemaxon.struc.CTransform3D: Copy.
set(DPoint3) - Method in class chemaxon.struc.DPoint3: Set coordinates.
setAbsStereo(boolean) - Method in class chemaxon.struc.MoleculeGraph: Sets the absolute stereoconfiguration flag.
setAbsStereo(boolean) - Method in class chemaxon.struc.RgMolecule: Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
setAbsStereo(boolean) - Method in class chemaxon.struc.RxnMolecule: Sets the absolute stereoconfiguration flag for all the structures.
setAcidicpKaUpperLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the maximum acidic pKa (default: 20).
setActionB(int, String) - Method in class JMView: Sets the action string (URL or JavaScript expression) of a button.
setActionB(int, String) - Method in class MView: Sets the action string (URL or JavaScript expression) of a button.
setActionC(int, boolean, String) - Method in class JMView: Sets one of the two action strings (JavaScript expressions) of a checkbox.
setActionC(int, boolean, String) - Method in class MView: Sets one of the two action strings (JavaScript expressions) of a checkbox.
setAliasstr(String) - Method in class chemaxon.struc.MolAtom: Sets the alias string.
setArcAngle(double) - Method in class chemaxon.struc.graphics.MPolyline: Sets the central angle of the arc.
setArrow(boolean) - Method in class chemaxon.struc.graphics.MPolyline: Sets or unsets arrow mode.
setArrowFlags(int, int) - Method in class chemaxon.struc.graphics.MPolyline: Sets the flags.
setArrowLength(int, double) - Method in class chemaxon.struc.graphics.MPolyline: Sets the arrow head length.
setArrowWidth(int, double) - Method in class chemaxon.struc.graphics.MPolyline: Sets the arrow head width.
setAtno(int) - Method in class chemaxon.struc.MolAtom: Sets the atomic number.
setAtom(int, MolAtom) - Method in class chemaxon.struc.Sgroup: Sets the specified atom in the S-group graph.
setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Sets the specified atom in the S-group graph.
setAtom(int, MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Sets the specified atom in the S-group graph.
setAtomAlias(int, String) - Method in class JMSketch: Sets atom alias.
setAtomAlias(int, int, String) - Method in class JMView: Sets atom alias.
setAtomAlias(int, String) - Method in class MSketch: Sets atom alias.
setAtomAlias(int, int, String) - Method in class MView: Sets atom alias.
setAtomExtraLabel(int, String) - Method in class JMSketch: Sets extra atom label.
setAtomExtraLabel(int, int, String) - Method in class JMView: Sets extra atom label.
setAtomExtraLabel(int, String) - Method in class MSketch: Sets extra atom label.
setAtomExtraLabel(int, int, String) - Method in class MView: Sets extra atom label.
setAtomMap(int) - Method in class chemaxon.struc.MolAtom: Sets the atom-atom mapping number.
setAtomSetColor(int, int) - Method in class JMView: Sets the color of an atom set.
setAtomSetColor(int, int) - Method in class MView: Sets the color of an atom set.
setAtomSetSeq(int, int, int) - Method in class JMView: Sets the set sequence number of the atom.
setAtomSetSeq(int, int, int) - Method in class MView: Sets the set sequence number of a atom.
setAtomSetVisible(int, boolean) - Method in class JMView: Set the visibility of the specified atom set.
setAtomSetVisible(int, boolean) - Method in class MView: Set the visibility of the specified atom set.
setAtoms(MolAtom[]) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Sets the atoms.
setAttach(int) - Method in class chemaxon.struc.MolAtom: Sets attachment point information.
setAttach(int, Sgroup) - Method in class chemaxon.struc.MolAtom: Sets attachment point information for an S-group attachment atom.
setAttribute(String, String) - Method in class chemaxon.struc.MObject: Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MPolyline: Sets the value of an attribute.
setAttribute(String, String) - Method in class chemaxon.struc.graphics.MTextBox: Sets the value of an attribute.
setAutoScale(boolean) - Method in class JMSketch: Sets the autoscale property.
setAutoScale(boolean) - Method in class MSketch: Sets the autoscale property.
setAutoSize(boolean) - Method in class chemaxon.struc.graphics.MTextBox: Turns on/off automatic size calculation.
setBackground(Color) - Method in class chemaxon.struc.MObject: Sets the background color of the object.
setBasicpKaLowerLimit(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the minimum basic pKa (default: -10).
setBondSetColor(int, int) - Method in class JMView: Sets the color of a bond set.
setBondSetColor(int, int) - Method in class MView: Sets the color of a bond set.
setBondSetSeq(int, int, int, int) - Method in class JMView: Sets the set sequence number of a bond.
setBondSetSeq(int, int, int, int) - Method in class MView: Sets the set sequence number of a bond.
setBondSetSeqAll(int, int) - Method in class JMView: Sets the set sequence number for each bond.
setBondSetSeqAll(int, int) - Method in class MView: Sets the set sequence number for each bond.
setC(int, boolean) - Method in class JMView: Sets the state of a checkbox.
setC(int, boolean) - Method in class MView: Sets the state of a checkbox.
setCharge(int) - Method in class chemaxon.struc.MolAtom: Sets the charge.
setChartLabel(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Sets the chart checkbox label field.
setChartTitle(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Sets the chart title field.
setChirality(int, int) - Method in class chemaxon.struc.MoleculeGraph: Set chirality of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets the Cl- concentration (default: 0.1).
setCloridIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin: Sets the Cl- concentration (default: 0.1).
setColor(Color) - Method in class chemaxon.struc.MObject: Sets the color of the object.
setComment(String) - Method in class chemaxon.struc.Molecule: Sets the comment.
setConnectivity(int) - Method in class chemaxon.struc.Sgroup: Sets S-group connectivity.
setCorners(MPoint, MPoint) - Method in class chemaxon.marvin.sketch.modules.RectangleSM
setCorners(double, double, double, double) - Method in class chemaxon.struc.MolAtom: Used internally by MolPainter.
setCorners(MPoint, MPoint) - Method in class chemaxon.struc.graphics.MRectangle: Sets the corners.
setCursorPos(int, boolean) - Method in class chemaxon.struc.graphics.MTextBox: Sets the cursor position.
setDim(int) - Method in class chemaxon.struc.Molecule: Sets the dimension.
setDim(int) - Method in class chemaxon.struc.MoleculeGraph: Sets the dimension.
setDim(int) - Method in class chemaxon.struc.RgMolecule: Sets the dimension of the root structure and the R-groups.
setDim(int) - Method in class chemaxon.struc.RxnMolecule: Sets the dimension for all the structures.
setDoublePrecision(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the precision in the decimal format.
setDoublePrecision(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the double -> string conversion precision (maximal number of fraction digits) with zero-padding (12.56 -> 12.5600 if precision=4).
setDoublePrecision(int, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the double -> string conversion precision (maximal number of fraction digits).
setDraggedObject(MObject) - Method in class chemaxon.struc.MDocument: Sets the dragged object.
setEdge(int, CEdge) - Method in class chemaxon.struc.CGraph: Sets the edge at the specified index.
setEdge(int, CEdge) - Method in class chemaxon.struc.RgMolecule: Sets the edge at the specified index.
setEdge(int, CEdge) - Method in class chemaxon.struc.RxnMolecule: Sets the edge at the specified index.
setEdge(int, CEdge) - Method in class chemaxon.struc.SelectionMolecule: Sets the edge at the specified index.
setEndPosition(long) - Method in class chemaxon.struc.MDocument: Sets the end position of this document in the input file.
setEndPosition(long) - Method in class chemaxon.struc.Molecule: Sets the end position of this molecule in the input file.
setExtraLabel(String) - Method in class chemaxon.struc.MolAtom: Sets the extra atom label: "label" or "label1|label2".
setExtraLabelColor(long) - Method in class chemaxon.struc.MolAtom: Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
setFilePointer(long) - Method in class chemaxon.formats.MolInputStream: Sets file pointer and initializes buffer.
setFlags(int) - Method in class chemaxon.struc.MolAtom: Sets the flags.
setFlags(int, int) - Method in class chemaxon.struc.MolAtom: Sets the flags.
setFlags(int) - Method in class chemaxon.struc.MolBond: Sets bond type (3 bit), stereo (2+2+1 bit), topology (2 bit) and bond set (5 bit) information.
setFlags(int, int) - Method in class chemaxon.struc.MolBond: Sets bond type (3 bit), stereo (2+2+1 bit), and topology (2 bit) information.
setFlags(int) - Method in class chemaxon.struc.graphics.MPolyline: Sets the flags.
setFocus(MObject) - Method in class chemaxon.struc.MDocument: Focus to the specified object.
setForbiddenMap(int) - Method in class chemaxon.marvin.modules.AutoMapper: The given atom map id should not be assigned to any atom.
setGUIContracted(boolean) - Method in class chemaxon.struc.Molecule: Contracts some S-groups to use in GUI or expands for any other use.
setGUIStateRecursively(boolean) - Method in class chemaxon.struc.Sgroup: Sets the expanded/contracted state recursively.
setGeom3D(boolean) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Sets 3D geometry consideration.
setGrinvCC(long) - Method in class chemaxon.struc.CGraph: Sets the graph invariant change count.
setHybridizationState(int) - Method in class chemaxon.struc.MolAtom: Sets the hybridization state.
setIdentity() - Method in class chemaxon.struc.CTransform3D: Makes identity transformation.
setImplicitHcount(int) - Method in class chemaxon.struc.MolAtom: Sets the number of implicit hydrogens.
setInputFormat(String) - Method in class chemaxon.struc.MDocument: Sets the input file format.
setInputFormat(String) - Method in class chemaxon.struc.Molecule: Sets the input file format.
setInputFormat(String) - Method in class chemaxon.struc.RgMolecule: Sets the input file format.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ChargePlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the input molecule.
setInputMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the input molecule.
setL(int, String) - Method in class JMView: Sets a label.
setL(int, String) - Method in class MView: Sets a label.
setLicense(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the license key in the license manager if the given license key matches the plugin's license key.
setLineColor(Color) - Method in class chemaxon.struc.MObject: Sets the color of the object.
setList(int[], int) - Method in class chemaxon.struc.MolAtom: Sets the list elements.
setList(int[]) - Method in class chemaxon.struc.MolAtom: Sets the list elements.
setLocation(DPoint3) - Method in class chemaxon.struc.MolAtom: Sets the coordinates.
setLocation(DPoint3) - Method in class chemaxon.struc.MoleculeGraph: Set the origin of the molecule.
setLocation(DPoint3) - Method in class chemaxon.struc.RgMolecule: Set the origin of the molecule.
setLocation(DPoint3) - Method in class chemaxon.struc.RxnMolecule: Set the origin of the molecule.
setM(int, String) - Method in class JMView: Starts loading a molecule into the nth cell in a separate thread.
setM(int, String, String) - Method in class JMView: Starts loading a molecule into the nth cell in a separate thread.
setM(int, String) - Method in class MView: Starts loading a molecule into the nth cell in a separate thread.
setM(int, String, String) - Method in class MView: Starts loading a molecule into the nth cell in a separate thread.
setMProperty(int, String, String) - Method in class JMView: Sets an RDfile/SDfile property.
setMProperty(int, String, String) - Method in class MView: Sets an RDfile/SDfile property.
setMainMoleculeGraph(MoleculeGraph) - Method in class chemaxon.struc.MDocument: Sets the main molecule graph.
setMap(int) - Method in class chemaxon.marvin.modules.AutoMapper: Sets atom-atom maps in the RxnMolecule passed in setReaction( final RxnMolecule rm ) according to the mapId map.
setMappingMode(int) - Method in class chemaxon.marvin.modules.AutoMapper: Sets the mapping mode to be used in consequent reaction mappings.
setMassno(int) - Method in class chemaxon.struc.MolAtom: Sets the mass number.
setMassnoIfKnown(String) - Method in class chemaxon.struc.MolAtom: Sets the atomic weight for deuterium or tricium.
setMaxIons(int) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the maximum number of ionizable atoms to be considered.
setMaxRepetitions(int) - Method in class chemaxon.struc.MolAtom: Sets the maximum number of repetitions for a link node.
setMinRepetitions(int) - Method in class chemaxon.struc.MolAtom: Sets the minimum number of repetitions for a link node.
setMol(String) - Method in class JMSketch: Starts loading a molecule into the sketcher in a separate thread.
setMol(String, String) - Method in class JMSketch: Starts loading a molecule into the sketcher in a separate thread.
setMol(String) - Method in class JMView: Starts loading molecules in a separate thread.
setMol(String, String) - Method in class JMView: Starts loading molecules in a separate thread.
setMol(String) - Method in class MSketch: Starts loading a molecule into the sketcher in a separate thread.
setMol(String, String) - Method in class MSketch: Starts loading a molecule into the sketcher in a separate thread.
setMol(String) - Method in class MView: Starts loading molecules in a separate thread.
setMol(String, String) - Method in class MView: Starts loading molecules in a separate thread.
setMol(Molecule) - Method in class chemaxon.marvin.sketch.MoleculeSM: Sets the molecule reference stored in the object.
setMol(Molecule) - Method in class chemaxon.marvin.sketch.SketchMode: Sets the molecule reference stored in the object.
setMolProperty(String, String) - Method in class JMSketch: Sets an RDfile/SDfile property.
setMolProperty(String, String) - Method in class MSketch: Sets an RDfile/SDfile property.
setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.ElementalAnalyser: Specifies a molecule to calculate with.
setMolecule(MoleculeGraph) - Method in class chemaxon.calculations.TopologyAnalyser: Specifies a molecule to calculate with.
setMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the input molecule after standardization.
setMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the input molecule after an optional standardization.
setMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the input molecule after an optional standardization.
setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Sets microspecies calculation.
setMsCalc(boolean) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets calculation of microspecies distributions.
setMultiplier(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Sets the multiplier.
setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets the Na+, K+ concentration (default: 0.1).
setNaKIonConcentration(double) - Method in class chemaxon.marvin.calculations.logPPlugin: Sets the Na+, K+ concentration (default: 0.1).
setName(String) - Method in class chemaxon.struc.Molecule: Sets the molecule name.
setName(String) - Method in class chemaxon.struc.RgMolecule: Sets the name of the root molecule.
setNode(int, CNode) - Method in class chemaxon.struc.CGraph: Sets the node at the specified index.
setNode(int, CNode) - Method in class chemaxon.struc.RgMolecule: Sets the node at the specified index.
setNode(int, CNode) - Method in class chemaxon.struc.RxnMolecule: Sets the node at the specified index.
setNode0(int, CNode) - Method in class chemaxon.struc.CGraph: Sets the node at the specified index.
setNode0(int, CNode) - Method in class chemaxon.struc.Molecule: Sets the node at the specified index.
setNode0(int, CNode) - Method in class chemaxon.struc.SelectionMolecule: Sets the node at the specified index.
setNode1(CEdge, CNode) - Static method in class chemaxon.struc.CNode: Sets the first node of an edge.
setNode1(CEdge, CNode) - Static method in class chemaxon.struc.sgroup.SgroupAtom: Sets the first node of an edge.
setNode2(CEdge, CNode) - Static method in class chemaxon.struc.CNode: Sets the second node of an edge.
setNode2(CEdge, CNode) - Static method in class chemaxon.struc.sgroup.SgroupAtom: Sets the second node of an edge.
setObject(MObject, int) - Method in class chemaxon.struc.MDocument: Sets an object
setObject(MObject, int) - Method in class chemaxon.struc.MSelectionDocument: Sets an object
setObjectContainingSelection(MObject) - Method in class chemaxon.struc.MDocument: Sets the object that contains the selection.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.ChargePlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.TPSAPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.logPPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the input parameters for the plugin.
setParameters(Properties) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Sets the input parameters for the plugin.
setParentMolecule(Molecule) - Method in class chemaxon.struc.Sgroup: Sets the parent molecule.
setParity(int, int) - Method in class chemaxon.struc.MoleculeGraph: Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity.
setParity(int[]) - Method in class chemaxon.struc.MoleculeGraph: Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.
setParity(int, int) - Method in class chemaxon.struc.SelectionMolecule: Sets the parity for a selected atom.
setParity(int[]) - Method in class chemaxon.struc.SelectionMolecule: Sets the parity for the selection.
setPiece(String) - Method in class JMSketch: Sets the current piece.
setPiece(String) - Method in class MSketch: Sets the current piece.
setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MPolyline: Sets the points.
setPoints(MPoint[]) - Method in class chemaxon.struc.graphics.MTextBox: Sets the points.
setProperty(String, String) - Method in class chemaxon.struc.Molecule: Sets an RDfile/SDfile property.
setProperty(String, String) - Method in class chemaxon.struc.RgMolecule: Sets an RDfile/SDfile property in the root structure.
setPropertyObject(String, Object) - Method in class chemaxon.struc.Molecule: Sets an RDfile/SDfile property object.
setPropertyObject(String, Object) - Method in class chemaxon.struc.RgMolecule: Sets an RDfile/SDfile property in the root structure.
setQProp(String, Object) - Method in class chemaxon.struc.MolAtom: Sets a query property.
setQProp(String, int) - Method in class chemaxon.struc.MolAtom: Sets a query property as an integer.
setQueryAromaticity(int) - Method in class chemaxon.struc.MolAtom: Sets the aromatic/aliphatic query property.
setQuerystr(String) - Method in class chemaxon.struc.MolAtom: Assigns the query properties string to this atom while setting all necessary atom and query properties.
setQuerystr(String, int) - Method in class chemaxon.struc.MolAtom: Assigns the query properties string to this atom while setting all necessary atom and query properties.
setRadical(int) - Method in class chemaxon.struc.MolAtom: Sets the radical value.
setReaction(RxnMolecule) - Method in class chemaxon.marvin.modules.AutoMapper: Sets the current reaction to be mapped.
setReactionArrow(DPoint3[]) - Method in class chemaxon.struc.RxnMolecule: Sets the reaction arrow.
setReactionArrow() - Method in class chemaxon.struc.RxnMolecule: Sets the stored reaction arrow.
setReactionArrow0() - Method in class chemaxon.struc.RxnMolecule: Sets the stored reaction arrow 'arrowPoints' to its calculated value.
setReactionArrowType(int) - Method in class chemaxon.struc.RxnMolecule: Sets the reaction arrow type.
setReactionArrowType(String) - Method in class chemaxon.struc.RxnMolecule: Sets the reaction arrow type from type name.
setReactionStereo(int) - Method in class chemaxon.struc.MolAtom: Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
setRepeatingUnitAtom(MolAtom, boolean) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Adds or removes an atom to/from the list of paradigmatic repeating unit atoms.
setResidueAtomId(int) - Method in class chemaxon.struc.MolAtom: Sets the residue atom identifier.
setResidueSeq(int) - Method in class chemaxon.struc.MolAtom: Sets the residue sequence number.
setResidueType(int) - Method in class chemaxon.struc.MolAtom: Sets the residue type.
setRgroup(int) - Method in class chemaxon.struc.MolAtom: Sets the R-group index.
setRlogic(int, int) - Method in class chemaxon.struc.RgMolecule: Sets R-logic flags.
setRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule: Sets R-logic occurence range.
setRoot(Molecule) - Method in class chemaxon.struc.RgMolecule: Sets the root structure.
setRotation(double, double, double, double) - Method in class chemaxon.struc.CTransform3D: Sets the rotation components.
setRotationCenter(DPoint3) - Method in class chemaxon.struc.CTransform3D: Sets the rotation center
setSMARTS(String) - Method in class chemaxon.struc.MolAtom: Sets SMARTS query string data.
setScale(double) - Method in class JMSketch: Sets the magnification.
setScale(double) - Method in class MSketch: Sets the magnification.
setScale(double) - Method in class chemaxon.struc.CTransform3D: Sets the scale factor.
setSelected(boolean) - Method in class chemaxon.struc.MObject: Selects or unselects the object.
setSelected(boolean) - Method in class chemaxon.struc.MolAtom: Selects or unselects this atom.
setSelected(boolean) - Method in class chemaxon.struc.graphics.MChemicalStruct: Selects or unselects the object.
setSelected(boolean) - Method in class chemaxon.struc.graphics.MTextBox: Selects or unselects the text box.
setSelectedIndex(int) - Method in class JMView: Selects a molecule.
setSelectedIndex(int) - Method in class MView: Selects a molecule.
setSetColor(int, int) - Method in class JMView: Deprecated. as of Marvin 3.3, replaced by setAtomSetColor
setSetColor(int, int) - Method in class MView: Deprecated. as of Marvin 3.3, replaced by setAtomSetColor
setSetSeq(int, int, int) - Method in class JMView: Deprecated. as of Marvin 3.3, replaced by setAtomSetSeq
setSetSeq(int, int, int) - Method in class MView: Deprecated. as of Marvin 3.3, replaced by setAtomSetSeq
setSetSeq(int) - Method in class chemaxon.struc.MolAtom: Sets the atom set sequence number.
setSetSeq(int) - Method in class chemaxon.struc.MolBond: Sets the bond set.
setSetSeqs(int) - Method in class chemaxon.struc.MoleculeGraph: Sets the set sequence number of all atoms.
setSetVisible(int, boolean) - Method in class JMView: Deprecated. as of Marvin 3.3, replaced by setAtomSetVisible
setSetVisible(int, boolean) - Method in class MView: Deprecated. as of Marvin 3.3, replaced by setAtomSetVisible
setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.Sgroup: Sets the molecule graph.
setSgroupGraph(SelectionMolecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Sets the molecule graph.
setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.Molecule: Sets or unsets an S-group as a parent of an atom.
setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule: Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.
setSgroupParent(MolAtom, Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule: Sets or unsets an S-group as a parent of an atom in reactants, products or agents.
setSkip(int, double) - Method in class chemaxon.struc.graphics.MPolyline: Sets the distance of the (visible) head or tail from the corresponding line end point.
setStartPoint(MPoint) - Method in class chemaxon.marvin.sketch.modules.EFlowSM: Sets the start position of the arrow drawn.
setStartPoint(MPoint) - Method in class chemaxon.marvin.sketch.modules.LineSM: Sets the start position of the line drawn.
setStartPosition(long) - Method in class chemaxon.struc.MDocument: Sets the starting position of this document in the input file.
setStartPosition(long) - Method in class chemaxon.struc.Molecule: Sets the starting position of this molecule in the input file.
setStereo2Flags(CNode, CNode, int) - Method in class chemaxon.struc.MolBond: Sets double bond stereo information.
setStereoGroupNumber(int) - Method in class chemaxon.struc.MolAtom: Sets the stereochemical group number.
setStereoGroupType(int) - Method in class chemaxon.struc.MolAtom: Sets the stereochemical group type.
setSubType(int) - Method in class chemaxon.struc.Sgroup: Sets polymer S-group subtype.
setSubscript(String) - Method in class chemaxon.struc.Sgroup: Sets the subscript for non-superatom S-groups.
setSubscript(String) - Method in class chemaxon.struc.sgroup.MultipleSgroup: Sets the subscript.
setT(int, String) - Method in class JMView: Gets the value of a text field.
setT(int, String) - Method in class MView: Gets the value of a text field.
setTemperature(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the temperature (default: 298 Kelvin).
setText(String) - Method in class chemaxon.struc.graphics.MTextBox: Sets the text.
setThickness(double) - Method in class chemaxon.struc.graphics.MPolyline: Sets the line thickness.
setThread(Thread) - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Sets the thread field.
setTitle(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Sets the title field.
setTranslation(DPoint3) - Method in class chemaxon.struc.CTransform3D: Sets the translation components.
setTranslation(double, double, double) - Method in class chemaxon.struc.CTransform3D: Sets the translation components.
setType(int) - Method in class chemaxon.marvin.sketch.BondSM
setType(int) - Method in class chemaxon.struc.MolBond: Sets bond type and does valence checking for the endpoints.
setUserTypes(String) - Method in class chemaxon.marvin.calculations.logPPlugin: Sets user types.
setValenceError(boolean) - Method in class chemaxon.struc.MolAtom: Sets or clears the valence error flag.
setValenceProp(int) - Method in class chemaxon.struc.MolAtom: Sets the valence property.
setVisible(boolean) - Method in class MSketch: Show or hide the applet.
setVisible(boolean) - Method in class MView: Show or hide the applet.
setX(double) - Method in class chemaxon.struc.MolAtom: Sets the X coordinate.
setXState(int) - Method in class chemaxon.struc.Sgroup: Sets the expanded/contracted state.
setXY(double, double) - Method in class chemaxon.struc.MolAtom: Sets the x and y coordinates.
setXYZ(double, double, double) - Method in class chemaxon.struc.MPoint: Sets the coordinates.
setXYZ(double, double, double) - Method in class chemaxon.struc.MolAtom: Sets the coordinates.
setXYZ(double, double, double) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Sets the atom coordinates.
setY(double) - Method in class chemaxon.struc.MolAtom: Sets the Y coordinate.
setZ(double) - Method in class chemaxon.struc.MolAtom: Sets the Z coordinate.
setpH(double) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Sets the pH: majority microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.
setpH(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets a single pH value for the logD calculation.
setpH(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets the pH value for the calculation of microspecies distributions.
setpHLower(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Sets pH lower limit for the calculation of microspecies distributions.
setpHLower(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets pH lower limit (default: 0.0).
setpHLower(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets pH lower limit for the calculation of microspecies distributions.
setpHStep(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Sets pH step for the calculation of microspecies distributions.
setpHStep(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets pH step to be taken between the pH lower and upper limits (default: 1.0).
setpHStep(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets pH step for the calculation of microspecies distributions.
setpHUpper(double) - Method in class chemaxon.marvin.calculations.HBDAPlugin: Sets pH upper limit for the calculation of microspecies distributions.
setpHUpper(double) - Method in class chemaxon.marvin.calculations.logDPlugin: Sets pH upper limit (default: 14.0).
setpHUpper(double) - Method in class chemaxon.marvin.calculations.pKaPlugin: Sets pH upper limit for the calculation of microspecies distributions.
sgroupGraph - Variable in class chemaxon.struc.Sgroup: The S-group's internal structure.
sgroupType - Variable in class chemaxon.struc.Sgroup: The S-group type.
skip(long) - Method in class chemaxon.formats.MolInputStream: Skips over and discards n bytes of data.
skipToNext() - Method in class chemaxon.marvin.modules.MolImport: Skips the remaining parts of the current molecule and positions the file pointer to the next one.
skipToNext() - Method in interface chemaxon.marvin.util.MolImportIface: Skips the remaining parts of the current molecule and positions the file pointer to the next one.
smallestRingSize() - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the size of the smallest ring in the molecule.
smallestRingSizeOfAtom(int) - Method in class chemaxon.calculations.TopologyAnalyser: Calculates the size of the smallest ring an atom is a member of.
sort(Sgroup[], int) - Static method in class chemaxon.struc.Sgroup: Sorts S-groups in parent-child or child-parent order.
sortEdgesAccordingTo(CEdge[]) - Method in class chemaxon.struc.CGraph: Sorts edges in the same order as they appear in another chemical graph.
sortEdgesAccordingTo(CEdge[]) - Method in class chemaxon.struc.RgMolecule: Sort edges in the same order as they appear in the specified array.
sortEdgesAccordingTo(CEdge[]) - Method in class chemaxon.struc.RxnMolecule: Sort edges in the same order as they appear in the specified array.
sringsize() - Method in class chemaxon.struc.CNode: Calculate the size of smallest ring containing this atom.
sssr - Variable in class chemaxon.struc.CGraph: SSSR ring node indexes.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin: Prevents default standardization: does nothing.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin: Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin: Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin: Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin: Prevents default standardization: does nothing.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin: Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin: Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin: Standardizes the molecule.
standardize(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).
standardizeGroups(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin: Default standardization: nitro groups: [O-]-[N+] >> O=N sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
start() - Method in class JMSketch: Starts the applet.
start() - Method in class JMView: Starts the applet.
start() - Method in class MSketch: Starts the applet.
start() - Method in class MView: Starts the applet.
startPoint - Variable in class chemaxon.marvin.sketch.modules.RectangleSM
stepWedge() - Method in class chemaxon.struc.MolBond: Set the bond from 0 to UP or UP to DOWN.
stepWedge(MolBond[]) - Static method in class chemaxon.struc.MolBond: Flip the given bonds to the next state ONLY 1 bond is set to chiral starting from the last bond
stereoClean() - Method in class chemaxon.struc.MoleculeGraph: Reset the wedges of the molecule, based on the actual parity information.
stop() - Method in class JMSketch: Hide the frames when stopped.
stop() - Method in class JMView: Stops the applet.
stop() - Method in class MSketch: Hide the frames when stopped.
stop() - Method in class MView: Stops the applet.
stringBuffer - Variable in class chemaxon.marvin.util.MolExportModule: This buffer can contain the molecule file contents, in case of a text format.
superGraph - Variable in class chemaxon.struc.CGraph: Parent of all parents.
swap() - Method in class chemaxon.struc.CEdge: Change orientation.
swapNodes(int, int) - Method in class chemaxon.struc.SelectionMolecule: Swap two nodes.
symbolOf(int) - Static method in class chemaxon.struc.MolAtom: Gets the element symbol for the specified atomic number.

T

TAIL - Static variable in class chemaxon.struc.graphics.MPolyline: Arrow tail (feather).
TEXTMODE - Static variable in class chemaxon.formats.MdlCompressor: Deprecated. as of Marvin 3.1, there is no possibility to do that
THICKNESS_SET_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline: Thickness is set flag.
TOPOLOGY_CHAIN - Static variable in class chemaxon.struc.MolBond: Bond is in a chain.
TOPOLOGY_MASK - Static variable in class chemaxon.struc.MolBond: Bond topology mask.
TOPOLOGY_RING - Static variable in class chemaxon.struc.MolBond: Bond is in a ring.
TPSAPlugin - class chemaxon.marvin.calculations.TPSAPlugin.: Plugin class for TPSA (topological polar surface area) calculation.
TPSAPlugin() - Constructor for class chemaxon.marvin.calculations.TPSAPlugin: Constructor.
TRANS - Static variable in interface chemaxon.struc.StereoConstants: Trans double bond.
TRANSFORM_DISTORT - Static variable in class chemaxon.struc.MObject: Distorting transformations are allowed.
TYPE_DISTR - Static variable in class chemaxon.marvin.calculations.pKaPlugin: Type constant for microspecies distribution.
TYPE_MASK - Static variable in class chemaxon.struc.MolBond: The lowest bits of the flags that store the bond type.
TYPE_MASK - Static variable in class chemaxon.struc.RxnMolecule: Structure type mask.
TextBoxSM - class chemaxon.marvin.sketch.modules.TextBoxSM.: Text box creation mode.
TextBoxSM() - Constructor for class chemaxon.marvin.sketch.modules.TextBoxSM: Constructs a text box object for sketching.
TextBoxSM(TextBoxSM) - Constructor for class chemaxon.marvin.sketch.modules.TextBoxSM: Copy constructor.
TopologyAnalyser - class chemaxon.calculations.TopologyAnalyser.: Central class for accessing functions analysing the topology of a molecule.
TopologyAnalyser() - Constructor for class chemaxon.calculations.TopologyAnalyser
TopologyAnalyserPlugin - class chemaxon.marvin.calculations.TopologyAnalyserPlugin.: Calculates topological data.
TopologyAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.TopologyAnalyserPlugin
toBinFormat(String) - Method in class chemaxon.struc.Molecule: Creates a binary representation of the molecule.
toFormat(String) - Method in class chemaxon.struc.Molecule: Creates a string representation of the molecule.
toObject(String) - Method in class chemaxon.struc.Molecule: Creates a String, byte[] array or Image representation of the molecule.
toString() - Method in class chemaxon.struc.CEdge: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.CGraph: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.CNode: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.CTransform3D: Gets a string representation of the matrix.
toString() - Method in class chemaxon.struc.DPoint3: Gets a string representation of the point
toString() - Method in class chemaxon.struc.MolAtom: Overrides Object.toString() to ease debugging.
toString() - Method in class chemaxon.struc.Sgroup: Overrides Object.toString() to ease debugging.
transform(DPoint3) - Method in class chemaxon.struc.CTransform3D: Transforms a point.
transform(CTransform3D) - Method in class chemaxon.struc.MDocument: Transforms all object's coordinates.
transform(CTransform3D, int) - Method in class chemaxon.struc.MDocument: Transforms all object's coordinates.
transform(CTransform3D, int) - Method in class chemaxon.struc.MObject: Transforms the object.
transform(CTransform3D, int) - Method in class chemaxon.struc.MPoint: Transforms all points.
transform(CTransform3D) - Method in class chemaxon.struc.MoleculeGraph: Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.MoleculeGraph: Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.RgMolecule: Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, boolean) - Method in class chemaxon.struc.RxnMolecule: Apply a transformation matrix to the atomic coordinates and the reaction arrow.
transform(CTransform3D) - Method in class chemaxon.struc.SelectionMolecule: Apply a transformation matrix to the atomic coordinates.
transform(CTransform3D, int) - Method in class chemaxon.struc.graphics.MAtomSetPoint: Does not perform any operation.
transform(CTransform3D, int) - Method in class chemaxon.struc.graphics.MChemicalStruct: Transforms all points.
transform(CTransform3D, int) - Method in class chemaxon.struc.graphics.MPolyline: Transforms all points, scales the arrow head widths and lengths.
transform(CTransform3D, int) - Method in class chemaxon.struc.graphics.MTextBox: Transforms all points and scales the font size.
transformCT(CNode, CNode, int) - Method in class chemaxon.struc.MolBond: Transform cis/trans stereo information into the `reference frame' of this bond.
transformReactionArrow(CTransform3D) - Method in class chemaxon.struc.RxnMolecule: Apply a transformation matrix to the reaction arrow.
twicesumbonds(boolean, boolean) - Method in class chemaxon.struc.MolAtom: Calculates the sum of bond orders.

U

UP - Static variable in class chemaxon.struc.MolBond: Single bond up.
ungroupSgroup(Sgroup) - Method in class chemaxon.struc.Molecule: Expand and ungroup the specified S-group.
ungroupSgroup(int) - Method in class chemaxon.struc.Molecule: Expand and ungroup the specified S-group.
ungroupSgroups() - Method in class chemaxon.struc.Molecule: Expand and ungroup all S-groups.
unhighlight(MObject) - Method in class chemaxon.struc.MDocument: Unhighlights an object.
unhighlightAll() - Method in class chemaxon.struc.MDocument: Unhighlights all objects.
unselectContents() - Method in class chemaxon.struc.MObject: Unselects sub-objects.
unselectContents() - Method in class chemaxon.struc.graphics.MChemicalStruct: Unselects atoms.
unselectContents() - Method in class chemaxon.struc.graphics.MPolyline: Unselects the points.
unselectContents() - Method in class chemaxon.struc.graphics.MTextBox: Unselects text.
updateParameters() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Updates parameters from parameter panel.
updateSgroupCrossings() - Method in class chemaxon.struc.sgroup.SuperatomSgroup: Deprecated. as of Marvin 3.3, replaced by Sgroup.findCrossingBonds()

V

VALCHK_ATTACH - Static variable in class chemaxon.struc.MolAtom: Deprecated. as of Marvin 3.5, attachment points are always checked
VALENCE_CHECKED - Static variable in class chemaxon.struc.MolAtom: Valence checked if this flag is set.
valenceCheck() - Method in class chemaxon.struc.MolAtom: Valence checking.
valenceCheck(int) - Method in class chemaxon.struc.MolAtom: Valence checking.
valenceCheck() - Method in class chemaxon.struc.MoleculeGraph: Check valence and query property errors.
valenceCheck(Vector) - Method in class chemaxon.struc.MoleculeGraph: Check valence and query property errors.
validate(String) - Method in class chemaxon.marvin.plugin.CalculatorPlugin: Validates the plugin.
verifyParameters() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader: Verifies parameters on the parameter panel.

W

write16doubles(ObjectOutput) - Method in class chemaxon.struc.CTransform3D: Writes the 4x4 matrix components as double precision floating point numbers.
write16floats(ObjectOutput) - Method in class chemaxon.struc.CTransform3D: Writes the 4x4 matrix components as single precision floating point numbers.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.CTransform3D: Serializes a transformation matrix.
writeExternal(ObjectOutput) - Method in class chemaxon.struc.DPoint3: Serializes a 3D point.

X

XSTATE_C - Static variable in class chemaxon.struc.Sgroup: S-group is contracted (useful only in GUI!).
XSTATE_NONE - Static variable in class chemaxon.struc.Sgroup: S-group is in an undetermined state.
XSTATE_X - Static variable in class chemaxon.struc.Sgroup: S-group is expanded.
XSTATE_XC - Static variable in class chemaxon.struc.Sgroup: S-group is expanded but its atoms have the same coordinates as in contracted state.
x - Variable in class chemaxon.struc.DPoint3: The x coordinate.
xCoordinate - Variable in class chemaxon.struc.MolAtom: X coordinate.

Y

y - Variable in class chemaxon.struc.DPoint3: The y coordinate.
yCoordinate - Variable in class chemaxon.struc.MolAtom: Y coordinate.

Z

z - Variable in class chemaxon.struc.DPoint3: The z coordinate.
zCoordinate - Variable in class chemaxon.struc.MolAtom: Z coordinate.

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