A B C D E F G H I J L M N O P Q R S T U V X Y Z

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.

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.

ARROW - Static variable in class chemaxon.struc.MolBond

Reaction arrow.

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 int 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.

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.

addCdataAttributeKeys(Vector) - Method in class chemaxon.struc.MObject

Adds attribute names to the specified vector.

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.

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.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.

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

Adds S-groups to this object and its parent.

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 wether the molecule has multiple chiral centres

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.

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.

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

Aromatize or dearomatize molecule.

B

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

Constant denoting basic pKa.

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

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

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.

C

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.

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.

CNode - class chemaxon.struc.CNode.

Node in a chemical graph.

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

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 bound 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.

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.

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.

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.

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.ChargePlugin

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Checks the input molecule.

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

Checks the input molecule.

checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.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.

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.plugin - package chemaxon.marvin.plugin

Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.

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.sgroup - package chemaxon.struc.sgroup

S-group related classes and interfaces.

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

Calculates atom coordinates.

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.

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

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

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.

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.MSelectionDocument

Creates a clone.

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

Clones the atom.

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

Make a copy of this object.

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

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.RgMolecule

Make an identical copy of the molecule.

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

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.sgroup.SgroupAtom

Clones the S-group superatom.

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

Clones the S-group superatom partially.

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.

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.

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(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.

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

Make a copy of this S-group.

copy(Sgroup, Molecule) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Make a copy of this S-group.

copy(CNode) - Method in class chemaxon.struc.sgroup.SgroupAtom

Make a copy of this S-group superatom.

copy(Sgroup, Molecule) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Make a copy of this S-group.

copyFromSgroupCopy(CNode) - Method in class chemaxon.struc.sgroup.SgroupAtom

Make a copy of this S-group superatom.

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.

createMol(String) - Static method in class chemaxon.struc.RgMolecule

Create molecule object for the specified input file format.

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

Creates a molecule object that contains only this group.

createReaction(Molecule, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule

Creates a reaction.

createStandardizedMolecule(Molecule) - 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.

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.

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

The default value of the number of ionizable atoms to consider.

DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph

Dimension bits in flags.

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.

dehydrogenize(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin

Makes all explicit H-s implicit.

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'.

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) - Method in class chemaxon.struc.MPoint

Gets the 2D distance from the specified point.

draw(Graphics, String) - Method in class chemaxon.struc.Molecule

Draws the molecule into a graphics context.

E

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.pKaPlugin

The microspecies is ignored if its distribution is less than EPSILON for all pH values.

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.

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

Expands all S-groups.

expandSgroups() - 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.

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.

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.

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

Finds R-group R#.

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

Finds the S-group that contains the specified node.

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

Finds the S-group related to the specified node.

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.

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.

G

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.

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.

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.

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

Gets the atomic number.

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.

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

Create an array of atoms.

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

Gets the array of atoms in the S-group.

getAtomCount(int) - Method in class JMView

Get number of atoms in the specified molecule cell.

getAtomCount(int) - Method in class MView

Get number of atoms in the specified molecule cell.

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.

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.

getAtomLabels(boolean, int, boolean, int[]) - Method in class chemaxon.struc.MolAtom

Gets the string representation of the atom labels.

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.

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.

getAutoScale() - Method in class JMSketch

Returns the autoscale property.

getAutoScale() - Method in class MSketch

Returns the autoscale property.

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.

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.

getCalcrgb(int) - Method in class chemaxon.struc.MolAtom

Gets the calculation result color: (alpha<<24 + red<<16 + green<<8 + blue).

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

Gets the calculation result color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

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

Gets the calculation result string: "result" or "result1|result2".

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.

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

Gets the charge.

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.

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.

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

Gets the color of the object.

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

Gets the comment.

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.

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.

getDoublePrecision() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the precision.

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

Gets the dragged object

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.

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.

getEdgeVector() - Method in class chemaxon.struc.CGraph

Gets the edges.

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.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).

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).

getErrorMessage() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).

getException() - Method in class chemaxon.marvin.plugin.PluginException

Returns the wrapped exception.

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

Gets number of hydrogen connections.

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.

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

Gets the focused object

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.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.

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.

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.

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.

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.IonChargePlugin

Returns the built-in license key for the given plugin class.

getLicenseKey() - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.

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.

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

Gets the main molecule graph.

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

Gets the atomic weight.

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

Calculates the molecular weight of the molecule.

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

Calculates the molecular weight of the molecule.

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

Calculates the molecular weight of the molecule.

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

Gets the mass number.

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.

getMolInputStream() - Method in interface chemaxon.marvin.util.MDocumentImportIface

Gets the molecule input stream.

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.

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() - 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.

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.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.

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.

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.

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

Gets the number of points.

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

Gets the number of points.

getPointRef(int) - 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.

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

Gets the number of point references.

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

Gets the number of point references.

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

Gets an array containing the atom coordinates.

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.

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.

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

Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.

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.

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.

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, 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.PolarizationPlugin

Returns the result item for the specified type 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.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.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.IonChargePlugin

Returns the specified result in String format.

getResultAsString(Object, int, Object) - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.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 key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.IonChargePlugin

Returns the number of result items for the given result key.

getResultCount(Object) - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.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.IonChargePlugin

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

getResultDomain(Object) - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.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.IonChargePlugin

Returns the result types (possible type: "charge").

getResultTypes() - Method in class chemaxon.marvin.calculations.PolarizationPlugin

Returns the result types (possible types: sigma, pi, total).

getResultTypes() - Method in class chemaxon.marvin.calculations.TPSAPlugin

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.

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.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.

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.

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.

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.

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.

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

Gets the simplified molecule object.

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

Gets the simplified molecule object.

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.

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.

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.

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.

getThread() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader

Returns the thread field.

getTitle() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader

Returns the title field.

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.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.

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

Gets the x coordinate.

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

Gets the X coordinate.

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.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.

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

Gets the y coordinate.

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

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.

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.

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

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.

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

True if the atom has aromatic bond.

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

Can the object have a background?

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)?

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?

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

Does it have query properties?

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

True if the atom has query bonds ("ANY" bonds).

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

Is it a SMARTS query atom?

hasSMARTSPropsExcluding(String) - Method in class chemaxon.struc.MolAtom

Is it a SMARTS query atom?

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

Determines if this atom has a valence error.

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.

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.

initMolImport(MolInputStream, String) - Method in interface chemaxon.marvin.util.MolImportIface

Initialization.

insideLabel(double, double) - Method in class chemaxon.struc.MolAtom

Determine if 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.

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

Checks if this edge represents a reaction arrow or not.

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

Returns true 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.

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 bond is connected to another one or not.

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?

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?

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?

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

Is the specified object currently highlighted?

isImplicitizableH(int) - Method in class chemaxon.struc.MolAtom

Determine if the hydrogen atom is implicitizable or not.

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

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?

isLicensed() - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Returns true if the plugin is licensed (has a license key).

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.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

True if the atom is a pseudo atom.

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

Determine wether is a query property or not

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

Is it a query atom?

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.

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

Is this bond in ring?

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

Determines if 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.

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.

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).

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.

MDocumentImportIface - interface chemaxon.marvin.util.MDocumentImportIface.

Marvin document reader interface.

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.

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.

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

MView - class MView.

AWT version of the MarvinView Applet.

MView() - Constructor for class MView

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(MolAtom, MolAtom) - Constructor for class chemaxon.struc.MolBond

Construct a single bond between two atoms.

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

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.

MultipleSgroup - class chemaxon.struc.sgroup.MultipleSgroup.

S-group.

MultipleSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.MultipleSgroup

Constructs a multiple S-group.

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

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.

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.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.

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.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.

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

Gets a new Sgroup instance.

newInstance() - Method in class chemaxon.struc.sgroup.MultipleSgroup

Gets a new MultipleSgroup instance.

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

Gets a new SuperatomSgroup instance.

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

objectContainingSelection - Variable in class chemaxon.struc.MDocument

objects - Variable in class chemaxon.struc.MDocument

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.

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.

PRODUCTS - Static variable in class chemaxon.struc.RxnMolecule

"Product" structure type.

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.

PolarizationPlugin - class chemaxon.marvin.calculations.PolarizationPlugin.

Plugin class for atom polarization calculation.

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

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.

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.util.MolExportModule

Parses the following option in the option string.

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.

preload() - Method in class chemaxon.marvin.plugin.CalculatorPluginLoader

Loads the calculator plugin.

printStackTrace(PrintStream) - 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.calculations.pKaPlugin

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.

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.

RgMolecule - class chemaxon.struc.RgMolecule.

A molecule or reaction containing R-groups.

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

Creates an RgMolecule.

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.

readDocument(MDocument) - Method in interface chemaxon.marvin.util.MDocumentImportIface

Reads the next document.

readLine() - Method in class chemaxon.formats.MolInputStream

Reads a line.

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[]) - Method in class chemaxon.struc.RxnMolecule

Sets the reaction arrow.

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

Recalculates the reaction arrow, forced recalculation.

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.Sgroup

Removes an atom 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.

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.

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

Removes the edge references.

removeGroupedAtom(Molecule, 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.

removeNode(int, int) - Method in class chemaxon.struc.CGraph

Removes a node and its edges from the graph.

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.

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

Removes a node and its edges.

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.

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

Change parents of all S-groups in this molecule.

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.

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.

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.

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.IonChargePlugin

Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH.

run() - Method in class chemaxon.marvin.calculations.PolarizationPlugin

Runs the charge calculation.

run() - Method in class chemaxon.marvin.calculations.TPSAPlugin

Runs the logP calculation.

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.

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.

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.

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.

StereoConstants - interface chemaxon.struc.StereoConstants.

Constants for atom parity and double bond stereo.

SuperatomSgroup - class chemaxon.struc.sgroup.SuperatomSgroup.

S-group.

SuperatomSgroup(Molecule, boolean) - Constructor for class chemaxon.struc.sgroup.SuperatomSgroup

Constructs a superatom S-group.

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.

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.

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.

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.

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.

setAttach(int) - Method in class chemaxon.struc.MolAtom

Sets attachment point information.

setAttribute(String, String) - Method in class chemaxon.struc.MObject

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.

setBackground(Color) - Method in class chemaxon.struc.MObject

Sets the background color of the object.

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.

setCalcrgbs(long) - Method in class chemaxon.struc.MolAtom

Sets the calculation color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

setCalcstr(String) - Method in class chemaxon.struc.MolAtom

Sets the calculation result string: "result" or "result1|result2".

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.

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(double, double, double, double) - Method in class chemaxon.struc.MolAtom

Used internally by MolPainter.

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, 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.

setEdge0(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.

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.

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

Focus to the specified object.

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.IonChargePlugin

Sets the input molecule.

setInputMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.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.

setM(int, String, String) - Method in class JMView

Starts loading a molecule into the nth cell.

setM(int, String) - Method in class MView

Starts loading a molecule into the nth cell.

setM(int, String, String) - Method in class MView

Starts loading a molecule into the nth cell.

setMainMoleculeGraph(MoleculeGraph) - Method in class chemaxon.struc.MDocument

Sets the main molecule graph.

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.

setMol(String) - Method in class JMSketch

Starts loading a molecule into the sketcher.

setMol(String, String) - Method in class JMSketch

Starts loading a molecule into the sketcher.

setMol(String) - Method in class MSketch

Starts loading a molecule into the sketcher.

setMol(String, String) - Method in class MSketch

Starts loading a molecule into the sketcher.

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.

setMultiplier(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Sets the multiplier.

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.IonChargePlugin

Sets the input parameters for the plugin.

setParameters(Properties) - Method in class chemaxon.marvin.calculations.PolarizationPlugin

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.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.

setPiece(String) - Method in class JMSketch

Sets the current piece.

setPiece(String) - Method in class MSketch

Sets the current piece.

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

Sets the query properties string.

setRadical(int) - Method in class chemaxon.struc.MolAtom

Sets the radical value.

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.

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.

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.

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.

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.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.

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.

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.

setY(double) - Method in class chemaxon.struc.MolAtom

Sets the Y coordinate.

setZ(double) - Method in class chemaxon.struc.MolAtom

Sets the Z coordinate.

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 interface chemaxon.marvin.util.MolImportIface

Skips the remaining parts of the current molecule and positions the file pointer to the next one.

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.IonChargePlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin

Standardizes the molecule.

standardize(Molecule) - Method in class chemaxon.marvin.calculations.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, ...).

standardizeNitro(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin

Standardizes nitro groups: [O-]-[N+]=O >> O=N=O.

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.

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

TEXTMODE - Static variable in class chemaxon.formats.MdlCompressor

Deprecated. as of Marvin 3.1, there is no possibility to do that

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.

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.

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

Deprecated. as of Marvin 3.0, replaced by getAtomSymbol and getAtomLabels

transform(DPoint3) - Method in class chemaxon.struc.CTransform3D

Transforms a point.

transform(CTransform3D) - Method in class chemaxon.struc.MDocument

transform(CTransform3D) - Method in class chemaxon.struc.MObject

Transforms the object.

transform(CTransform3D) - 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.

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.

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.

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

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() - 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.

X

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.

A B C D E F G H I J L M N O P Q R S T U V X Y Z