chemaxon.struc
Class MoleculeGraph

java.lang.Object
  chemaxon.struc.CGraph
      chemaxon.struc.MoleculeGraph

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable, StereoConstants

Direct Known Subclasses:

Molecule, SelectionMolecule

public class MoleculeGraph

extends CGraph

implements StereoConstants

A graph consisting of MolAtom vertices and MolBond edges.

Since:

3.0, 10/11/2002

Version:

3.3, 01/02/2004

Author:

Peter Csizmadia, Ferenc Csizmadia, Andras Volford, Gyorgy Pirok, Szilveszter Juhos

See Also:

MolAtom, MolBond, Serialized Form

Field Summary

protected static int	DIM_MASK Dimension bits in flags.
protected int	flags Stores the dimension (0, 2 or 3) and the chiral flag.
protected boolean	isMultiChiral true if there are at least two chiral centres
protected double	orix Origin x.
protected double	oriy Origin y.
protected double	oriz Origin z.
protected static int	RMCLEANUP_STEREO When removing a H atom, keep stereo information unchanged.

Fields inherited from class chemaxon.struc.CGraph

btab, ctab, edgeCount, edges, fragIds, grinv, grinvCC, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_NONE, sssr, superGraph

Fields inherited from interface chemaxon.struc.StereoConstants

ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS

Constructor Summary

MoleculeGraph()
Construct a molecule.

MoleculeGraph(MoleculeGraph p)
Construct a molecule or fragment.

MoleculeGraph(MoleculeGraph p, int na, int nb)
Construct a molecule or fragment with the specified number of atoms and bonds.

Method Summary

void	adjustMultiChiralFlag() Checks wether the molecule has multiple chiral centres
void	aromatize(boolean a) Aromatize or dearomatize molecule.
double	bondlength() Calculates the regular bond length.
DPoint3	calcCenter() Calculates the geometrical center.
void	calcCenter(DPoint3 p) Calculates the geometrical center.
int	calcDehydrogenizedGrinv(int[] gi) Calculates the graph invariants with the assumption that hydrogens are removed.
double	calcHeight() Calculates the molecule height.
void	calcOutRectCenter(DPoint3 p)
double	calcWidth() Calculates the molecule width.
boolean	canBeCT(int i2, int i3) Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
boolean	clean(int dim, java.lang.String opts) Calculates atom coordinates.
void	clear() Clears the molecule.
void	clearForImport(java.lang.String format) Clears the edges vector, the properties, the flags, and sets the origin coordinates to 0.
java.lang.Object	clone() Make an identical copy of the molecule.
void	clonecopy(CGraph g) Make another molecule identical to this one.
void	clonelesscopy(CGraph g) Copy to selection.
boolean	contains(CGraph graph) Does the graph contain the specified fragment?
int[][]	createBHtab() Creates the bond table extended with implicit hydrogen atoms.
int[][]	createCHtab() Creates the connection table extended with implicit hydrogen atoms.
protected MoleculeGraph	createDehydrogenizedReadOnlyGraph() Creates a dehydrogenized version of the molecule.
int[][]	getAromrings() Get aromatic ring atom indexes.
int[][]	getAromrings(int size) Get aromatic ring atom indexes.
MolAtom	getAtom(int n) Gets the nth atom.
MolAtom[]	getAtomArray() Create an array of atoms.
int	getAtomCount() Gets the number of atoms.
MolBond	getBond(int n) Gets the nth bond.
int	getBondCount() Gets the number of bonds.
int	getChirality(int i) 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.
double	getDesiredLength(int atno1, int atno2, int type) Gets the ideal bond length in Angstroms.
double	getDesiredLength(MolBond b) Gets the ideal bond length in Angstroms.
int	getDim() Gets the dimension.
MDocument	getDocument() Gets the parent document object.
java.lang.String	getFormula() Gets the molecular formula.
MoleculeGraph	getGraphUnion() Gets a graph containing all the atoms and bonds.
int	getGrinv(int[] gi) Gets the graph invariants.
int	getGrinv(int[] gi, boolean uniqueFlag) Gets the graph invariants (canonical labels).
int	getImplicitHcount() Gets the total number of implicit hydrogens attached to the molecule.
DPoint3	getLocation() Gets the origin of the molecule.
double	getMass() Calculates the molecular weight of the molecule.
int[][]	getNonAromrings() Get alpihatic ring atom indexes.
int[][]	getNonAromrings(int size) Get alpihatic ring atom indexes.
int	getParity(int i) 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.
DPoint3[]	getPoints() Gets an array containing the atom coordinates.
int[]	getSSSRBondSet() Get SSSR bond bitsets in integer array.
int	getStereo2(CNode a1, int i2, int i3, CNode a4) Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
int	getStereo2(int i1, int i2, int i3, int i4) Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
int	getStereo2(MolBond b) Gets cis/trans (Z/E) stereo information for the given bond.
int	getStereo2(MolBond b, CNode a1, CNode a4) Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
int	getStereo2(MolBond b, CNode a1, CNode a4, boolean grcheck) Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
protected int	getStereo2(MolBond b, CNode a1, int i2, int i3, CNode a4) Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
protected int	getStereo2(MolBond b, CNode a1, int i2, int i3, CNode a4, boolean grcheck) Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
boolean	hasImplicitH() Indicates, whether the molecule has implicit hydrogen atoms.
boolean	hydrogenize(boolean add) Implicit/explicit Hydrogen conversion.
void	implicitizeHydrogens(int f) Removes explicit bound Hydrogens from the graph and converts them to implicit.
boolean	isAbsStereo() Gets the absolute stereoconfiguration flag.
boolean	isAtom() Determines whether the structure represents only one atom and an arbitrary number of bonds.
boolean	isBond() Determines whether the structure represents only one bond and zero or two atoms.
boolean	isMultiChiral() Returns the multiple chirality flag.
boolean	isRingBond(int idx) Is this bond in ring?
protected void	makeItSimilar(CGraph g) Copies some properties of this molecule to the other one specified as argument.
void	moveTo(DPoint3 o) Move the molecule.
CGraph	newInstance() Creates a new MoleculeGraph object.
void	qpropCheck(java.util.Vector v) Check for query property errors.
protected void	removeNode(CNode node, int cleanupFlags) Removes a node and its edges.
protected void	removeNode(int i, int cleanupFlags) Removes a node and its edges.
void	setAbsStereo(boolean c) Sets the absolute stereoconfiguration flag.
boolean	setChirality(int i, int c) 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.
void	setDim(int d) Sets the dimension.
void	setLocation(DPoint3 o) Set the origin of the molecule.
boolean	setParity(int[] p) Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.
boolean	setParity(int i, int p) Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity.
void	setSetSeqs(int id) Sets the set sequence number of all atoms.
boolean	stereoClean() Reset the wedges of the molecule, based on the actual parity information.
void	transform(CTransform3D t) Apply a transformation matrix to the atomic coordinates.
protected void	transform(CTransform3D t, boolean incg) Apply a transformation matrix to the atomic coordinates.
void	valenceCheck() Check valence and query property errors.
void	valenceCheck(java.util.Vector v) Check valence and query property errors.

Methods inherited from class chemaxon.struc.CGraph

add, add, addEdge0, addEdgeWithoutChangingIt, addNode0, addNodeWithoutChangingIt, contains, findFrag, findFrags, fuse, fuse0, getBtab, getCtab, getEdge, getEdgeCount, getEdgeVector, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getNodeVector, getParent, getSSSR, indexOf, indexOf, isEmpty, isRealNodeParent, mergeNodes, pack, regenEdges, removeAll, removeAllEdges, removeEdge, removeEdge, removeEdge, removeEdge, removeNode, removeNode, resetCtab, resetGrinvInParents, setEdge, setNode, setNode0, toString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DIM_MASK

protected static final int DIM_MASK

Dimension bits in flags.

See Also:

flags, Constant Field Values

RMCLEANUP_STEREO

protected static final int RMCLEANUP_STEREO

When removing a H atom, keep stereo information unchanged.

Since:

3.1

See Also:

removeNode(CNode, int), removeNode(int, int), CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, Constant Field Values

orix

protected transient double orix

Origin x.

oriy

protected transient double oriy

Origin y.

oriz

protected transient double oriz

Origin z.

flags

protected transient int flags

Stores the dimension (0, 2 or 3) and the chiral flag.

See Also:

getDim(), isAbsStereo()

isMultiChiral

protected transient boolean isMultiChiral

true if there are at least two chiral centres

Constructor Detail

MoleculeGraph

public MoleculeGraph(MoleculeGraph p,
                     int na,
                     int nb)

Construct a molecule or fragment with the specified number of atoms and bonds.

Parameters:

p - the molecule that contains the created fragment

na - no reallocation needed until the number of atoms is less than this value

nb - no reallocation needed until the number of bonds is less than this value

MoleculeGraph

public MoleculeGraph(MoleculeGraph p)

Construct a molecule or fragment.

Parameters:

p - the parent structure

MoleculeGraph

public MoleculeGraph()

Construct a molecule.

Method Detail

getDocument

public MDocument getDocument()

Gets the parent document object.

Returns:

a Marvin document object

Since:

3.3

setDim

public void setDim(int d)

Sets the dimension.

Parameters:

d - 0, 2, or 3

See Also:

flags

getDim

public int getDim()

Gets the dimension.

Returns:

0, 2, or 3

See Also:

flags

isAbsStereo

public boolean isAbsStereo()

Gets the absolute stereoconfiguration flag. "Chiral flag" in MDL molfiles.

Returns:

true for absolute, false for relative configuration

See Also:

flags

setAbsStereo

public void setAbsStereo(boolean c)

Sets the absolute stereoconfiguration flag.

Parameters:

c - the absolute stereoconfiguration flag

See Also:

flags

clear

public void clear()

Clears the molecule. Does the same as clearForImport() but also clears the nodes vector.

See Also:

clearForImport(java.lang.String), CGraph.nodes

clearForImport

public void clearForImport(java.lang.String format)

Clears the edges vector, the properties, the flags, and sets the origin coordinates to 0. The molecule dimension is set to 2.

Parameters:

format - input file format, neglected

See Also:

CGraph.edges, orix, oriy, oriz, flags

removeNode

protected void removeNode(CNode node,
                          int cleanupFlags)

Removes a node and its edges.

Overrides:

removeNode in class CGraph

Parameters:

node - the node

cleanupFlags - extra clean-up methods

Since:

3.1

See Also:

CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, RMCLEANUP_STEREO

removeNode

protected void removeNode(int i,
                          int cleanupFlags)

Removes a node and its edges.

Overrides:

removeNode in class CGraph

Parameters:

i - the node index

cleanupFlags - extra clean-up methods

Since:

3.1

See Also:

CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, RMCLEANUP_STEREO

setSetSeqs

public void setSetSeqs(int id)

Sets the set sequence number of all atoms.

Parameters:

id - the set sequence number

Since:

2.9.1

hydrogenize

public boolean hydrogenize(boolean add)

Implicit/explicit Hydrogen conversion. Adds explicit H atoms instead of the current implicit ones, or removes explicit H atoms and increases the number of implicit hydrogens.

Parameters:

add - add explicit H atoms if true, remove if false

Returns:

true for success, false if an error occured

Throws:

java.lang.SecurityException - cannot load module because of a security problem (firewall)

implicitizeHydrogens

public void implicitizeHydrogens(int f)

Removes explicit bound Hydrogens from the graph and converts them to implicit. Only those explicit H atoms are converted for which MolAtom.isImplicitizableH(int) returns true.

Parameters:

f - flags specifying special H atom types to include

Since:

3.1

See Also:

MolAtom.LONELY_H, MolAtom.ISOTOPE_H, MolAtom.CHARGED_H, MolAtom.RADICAL_H, MolAtom.MAPPED_H

getGrinv

public int getGrinv(int[] gi)

Gets the graph invariants. The graph invariants are copied into the specified array, that must have the same length as the number of atoms in the molecule.

Notes: 1. For normal molecules and R-groups, graph invariants are recalculated only if an atom or bond changed, removed or added.
2. For selections, graph invariants are recalculated each time this function is called, because atoms and bonds cannot notify selections about their changes.

Overrides:

getGrinv in class CGraph

Parameters:

gi - output array, its length must be equal to the number of atoms

Returns:

the number of different graph invariants

Throws:

java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)

getGrinv

public int getGrinv(int[] gi,
                    boolean uniqueFlag)

Gets the graph invariants (canonical labels). Same like the former method but if the boolean flag is true chiral info is also added to invariants (needed for unique SMILES).

Parameters:

gi - output array, its length must be equal to the number of atoms

uniqueFlag - boolean flag

Returns:

the number of different graph invariants

Throws:

java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)

Since:

3.3

calcDehydrogenizedGrinv

public int calcDehydrogenizedGrinv(int[] gi)

Calculates the graph invariants with the assumption that hydrogens are removed. Entries corresponding to hydrogens are filled with -1 values in the output array. Only normal Hydrogen atoms are removed, isotopes (Deuterium and Tricium) are not.

Parameters:

gi - output array, its length must be equal to the number of atoms

Returns:

the number of different graph invariants

Throws:

java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)

Since:

3.1

See Also:

getGrinv(int[])

createDehydrogenizedReadOnlyGraph

protected MoleculeGraph createDehydrogenizedReadOnlyGraph()

Creates a dehydrogenized version of the molecule. The same atom and bond objects are used as in the original molecule, so the returned structure must be used for reading only. Hydrogen isotopes (Deuterium and Tricium) are not removed.

Returns:

dehydrogenized structure

Since:

3.1

valenceCheck

public void valenceCheck()

Check valence and query property errors.

See Also:

MolAtom.valenceCheck()

valenceCheck

public void valenceCheck(java.util.Vector v)

Check valence and query property errors. Check all the atoms if the argument is null.

Parameters:

v - contains the atoms to check

See Also:

MolAtom.valenceCheck()

qpropCheck

public void qpropCheck(java.util.Vector v)

Check for query property errors. Check all the atoms if the argument is null.

Parameters:

v - contains the atoms to check

See Also:

MolAtom.qpropCheck()

contains

public final boolean contains(CGraph graph)

Does the graph contain the specified fragment?

Overrides:

contains in class CGraph

Parameters:

graph - the fragment

Returns:

true if it contains the graph, false if not

isAtom

public boolean isAtom()

Determines whether the structure represents only one atom and an arbitrary number of bonds. Note: a one-atom structure has bonds only if it is a fragment.

Returns:

true if the number of nodes is one

isBond

public boolean isBond()

Determines whether the structure represents only one bond and zero or two atoms.

Returns:

true if the structure is the representation of a bond

getAtomCount

public final int getAtomCount()

Gets the number of atoms.

Returns:

number of atoms

getAtom

public MolAtom getAtom(int n)

Gets the nth atom.

Parameters:

n - the atom index

Returns:

the atom object

getBondCount

public final int getBondCount()

Gets the number of bonds.

Returns:

number of bonds

getBond

public MolBond getBond(int n)

Gets the nth bond.

Parameters:

n - the bond index

Returns:

the bond object

getAtomArray

public MolAtom[] getAtomArray()

Create an array of atoms.

Returns:

array of atom objects

Since:

2.6

calcCenter

public void calcCenter(DPoint3 p)

Calculates the geometrical center.

Parameters:

p - reference to the object that will hold the result

Since:

2.7

calcOutRectCenter

public void calcOutRectCenter(DPoint3 p)

calcCenter

public DPoint3 calcCenter()

Calculates the geometrical center.

Returns:

center point

calcWidth

public double calcWidth()

Calculates the molecule width.

Returns:

the molecule width

Since:

3.0

calcHeight

public double calcHeight()

Calculates the molecule height.

Returns:

the molecule height

Since:

3.0

getDesiredLength

public double getDesiredLength(int atno1,
                               int atno2,
                               int type)

Gets the ideal bond length in Angstroms.

Parameters:

atno1 - atomic number of first molecule

atno2 - atomic number of second molecule

type - bond type

Returns:

the ideal bond length

getDesiredLength

public double getDesiredLength(MolBond b)

Gets the ideal bond length in Angstroms.

Parameters:

b - the bond

Returns:

the ideal bond length

Since:

2.7

bondlength

public double bondlength()

Calculates the regular bond length.

Returns:

the calculated length in Angstroms, or MolBond.CCLENGTH if the molecule has no bonds

getLocation

public DPoint3 getLocation()

Gets the origin of the molecule.

Returns:

the origin

Since:

2.7

See Also:

orix

setLocation

public void setLocation(DPoint3 o)

Set the origin of the molecule.

Parameters:

o - the origin

Since:

2.7

See Also:

orix

moveTo

public void moveTo(DPoint3 o)

Move the molecule.

Parameters:

o - the new origin

Since:

2.7

See Also:

orix

transform

public void transform(CTransform3D t)

Apply a transformation matrix to the atomic coordinates.

Parameters:

t - the transformation matrix

Since:

2.7

transform

protected void transform(CTransform3D t,
                         boolean incg)

Apply a transformation matrix to the atomic coordinates.

Parameters:

t - the transformation matrix

incg - change graph invariants (true) or not (false)

Since:

3.0

getPoints

public DPoint3[] getPoints()

Gets an array containing the atom coordinates.

Returns:

atom coordinates array

Since:

2.9.1

clonecopy

public void clonecopy(CGraph g)

Make another molecule identical to this one.

Overrides:

clonecopy in class CGraph

Parameters:

g - the target molecule

clonelesscopy

public void clonelesscopy(CGraph g)

Copy to selection. Make another molecule identical to this one, but do not clone atoms, bonds, and the properties.

Overrides:

clonelesscopy in class CGraph

Parameters:

g - the target molecule object (the selection)

clone

public java.lang.Object clone()

Make an identical copy of the molecule.

Overrides:

clone in class CGraph

Returns:

the copy

getParity

public final int getParity(int i)

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. Leaves the imported parity unchanged.

Parameters:

i - the index of the atom whose parity is to be determined

Returns:

0 for nonchiral, PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_ODD|PARITY_EVEN for atoms whose parity is unspecified or cannot be assigned -as they are defined in MolAtom

Throws:

java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, isAbsStereo(), setAbsStereo(boolean)

setParity

public boolean setParity(int i,
                         int p)

Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity. If all atom parities will be set then setParity(int[] p) is more efficient.

Parameters:

i - the index of the atom whose parity is to be set

p - parity to be set (PARITY_ODD,PARITY_EVEN)

Returns:

true if successful

Throws:

java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, MolBond.UP, MolBond.DOWN, setParity(int[] p)

setParity

public boolean setParity(int[] p)

Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.

Parameters:

p - the parity for each atom in the molecule

Returns:

true if successful

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, isAbsStereo(), setAbsStereo(boolean), MolBond.UP, MolBond.DOWN

getChirality

public final int getChirality(int i)

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. Leaves the imported configuration unchanged.

Parameters:

i - the index of the atom whose chirality is to be determined

Returns:

0 for nonchiral, CHIRALITY_R or CHIRALITY_S for atoms of R or S configuration, PARITY_EITHER for atoms whose configuration is unspecified or cannot be assigned -as they are defined in MolAtom

Throws:

java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)

See Also:

StereoConstants.CHIRALITY_R, StereoConstants.CHIRALITY_S

setChirality

public boolean setChirality(int i,
                            int c)

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.

Parameters:

i - the index of the atom whose chirality is to be set

c - chirality to be set (CHIRALITY_R,CHIRALITY_S)

Returns:

true if successful

Throws:

java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)

See Also:

StereoConstants.CHIRALITY_R, StereoConstants.CHIRALITY_S

getStereo2

public final int getStereo2(int i1,
                            int i2,
                            int i3,
                            int i4)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Not checking atom equivalences using graph invariants.

Parameters:

i1 - index of atom A1

i2 - index of atom A2

i3 - index of atom A3

i4 - index of atom A4

Returns:

the cis/trans information, or 0 if A2 and A3 are not connected

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

getStereo2

public final int getStereo2(CNode a1,
                            int i2,
                            int i3,
                            CNode a4)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D.

Parameters:

a1 - atom A1

i2 - index of atom A2

i3 - index of atom A3

a4 - atom A4

Returns:

the cis/trans information, or 0 if A2 and A3 are not connected

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

getStereo2

public final int getStereo2(MolBond b,
                            CNode a1,
                            CNode a4)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Atoms A2 and A3 are node1 and node2 of the specified bond. Both (A2, A3) = (node1, node2) and (A2, A3) = (node2, node1) works. Not checking atom equivalences using graph invariants.

Parameters:

b - the bond

a1 - atom A1

a4 - atom A4

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

getStereo2

public final int getStereo2(MolBond b,
                            CNode a1,
                            CNode a4,
                            boolean grcheck)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Atoms A2 and A3 are node1 and node2 of the specified bond. Both (A2, A3) = (node1, node2) and (A2, A3) = (node2, node1) works.

Parameters:

b - the bond

a1 - atom A1

a4 - atom A4

grcheck - true if check atom equivalences using graph invariants

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

getStereo2

public final int getStereo2(MolBond b)

Gets cis/trans (Z/E) stereo information for the given bond. Use the CIP rules to determine the A1, A4 atoms in A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Not checking atom equivalences using graph invariants.

Parameters:

b - the bond

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

getStereo2

protected final int getStereo2(MolBond b,
                               CNode a1,
                               int i2,
                               int i3,
                               CNode a4)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Not checking atom equivalences using graph invariants.

Parameters:

b - the bond

a1 - atom A1

i2 - index of atom A2

i3 - index of atom A3

a4 - atom A4

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

getStereo2

protected final int getStereo2(MolBond b,
                               CNode a1,
                               int i2,
                               int i3,
                               CNode a4,
                               boolean grcheck)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D.

Parameters:

b - the bond

a1 - atom A1

i2 - index of atom A2

i3 - index of atom A3

a4 - atom A4

grcheck - true if check atom equivalences using graph invariants

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2()

canBeCT

public final boolean canBeCT(int i2,
                             int i3)

Determines whether the bond between the specified atoms can be a CIS/TRANS or not.

Parameters:

i2 - index of the first atom

i3 - index of the second atom

Returns:

true if this is a double bond that can be either CIS, TRANS or EITHER, false else.

aromatize

public void aromatize(boolean a)

Aromatize or dearomatize molecule.

Parameters:

a - aromatize (true) or dearomatize (false)

Throws:

java.lang.SecurityException - cannot load module because of a security problem (firewall)

Since:

2.8

getFormula

public java.lang.String getFormula()

Gets the molecular formula.

Returns:

the formula

getMass

public double getMass()

Calculates the molecular weight of the molecule. Returns a double value.

makeItSimilar

protected void makeItSimilar(CGraph g)

Copies some properties of this molecule to the other one specified as argument. Copies the flags and the origin coordinates.

Overrides:

makeItSimilar in class CGraph

Parameters:

g - the molecule to change

newInstance

public CGraph newInstance()

Creates a new MoleculeGraph object. The dimension and the origin coordinates will be the same as in the original molecule.

Overrides:

newInstance in class CGraph

Returns:

a MoleculeGraph object

getGraphUnion

public MoleculeGraph getGraphUnion()

Gets a graph containing all the atoms and bonds.

Returns:

this object (in the default implementation)

Since:

3.0, 11/11/2002

hasImplicitH

public boolean hasImplicitH()

Indicates, whether the molecule has implicit hydrogen atoms.

Returns:

true, if the molecule has at least one implicit hydrogen atom

clean

public boolean clean(int dim,
                     java.lang.String opts)

Calculates atom coordinates.

Parameters:

dim - dimensions

opts - cleaning options

• for 2D:

  O0 No optimization
  O1 Optimize if needed (default)
  O2 Always optimize

  e Verbose either flag
  

  If it is not possible to decide whether
  the double bond is CIS or TRANS, set the
  double bond to either

  d show debugging info

  tX set optimization time limit to X ms
  

  maximum time spend in the optimization
  default value: 5000ms
  if X<1, no time limit used

  iX set iteration limit to X step
  

  maximum iteration step in the optimization algorithm
  default value: 100

  rX set ring step limit to X step
  

  maximum number of steps when drawing a ring
  avoiding bond cross
  default value: no limit

  cX set branch step limit to X
  

  step limit for the recursively drawing
  a branch of a moleule avoiding bond cross
  default value: no limit

• for 3D:

  O0 Lightweight optimization (default)

  OD Dreiding optimization

null use the default values

Returns:

true for success, false if an error occured

Throws:

java.lang.SecurityException - cannot load module because of a security problem (firewall)

stereoClean

public boolean stereoClean()

Reset the wedges of the molecule, based on the actual parity information. Only rings smaller then 19 atoms are examined.

Returns:

true if succesful

getAromrings

public int[][] getAromrings()

Get aromatic ring atom indexes. Only rings smaller then 19 atoms are examined. Note: If you want to get the aliphatic rings also, get first them by using getNonAromrings and then the aromatic ones.

Returns:

the aromatic ring atom indexes.

getNonAromrings

public int[][] getNonAromrings()

Get alpihatic ring atom indexes. Only rings smaller then 19 atoms are examined. Getting the aliphatic rings is much slower then the aromatic ones.

Returns:

the nonaromatic ring atom indexes.

getAromrings

public int[][] getAromrings(int size)

Get aromatic ring atom indexes. Only rings smaller then the given size are examined. Note: If you want to get the aliphatic rings also, get first them by using getAliphaticrings and then the aromatic ones.

Parameters:

size - the maximum ring size during ring detection

Returns:

the aromatic ring atom indexes.

getNonAromrings

public int[][] getNonAromrings(int size)

Get alpihatic ring atom indexes. Only rings smaller then the given size are examined. Getting the aliphatic rings is much slower then the aromatic ones.

Parameters:

size - the maximum ring size during ring detection

Returns:

the aliphatic ring atom indexes.

getSSSRBondSet

public int[] getSSSRBondSet()

Get SSSR bond bitsets in integer array. To get if the given 'n' bond is in the sssr integer array 'r', use the following code:

 static boolean get(int n, int[] r) {
    return (r[n/32] & (((int)1) << (31-(n % 32)))) != 0 ;

 }
 

Returns:

the SSSR ring bond indexes in integer array.

isRingBond

public boolean isRingBond(int idx)

Is this bond in ring?

Parameters:

idx - the bond index

Returns:

true if the bond is in ring else false.

createCHtab

public int[][] createCHtab()

Creates the connection table extended with implicit hydrogen atoms. The implicit H atoms are indexed by free index numbers starting from the atom count and proceeding one-by-one from there. The current implementation always creates the table, the molecule does not store its extended connection table. chtab[i][j] will be the index of the jth neighbor of the ith atom, where atom indices greater than or equal to the atom count mean implicit hydrogen atoms.

Returns:

the chtab array

Since:

3.0

createBHtab

public int[][] createBHtab()

Creates the bond table extended with implicit hydrogen atoms. The implicit H atoms are indexed by free index numbers starting from the atom count and proceeding one-by-one from there. The current implementation always creates the table, the molecule does not store its extended connection table. bhtab[i][j] will be the index of the bond between atoms i and j, or -1 if there is no bond, -2 if it is an atom-implicitH bond where atom indices greater than or equal to the atom count mean implicit hydrogen atoms.

Returns:

the chtab array

Since:

3.0

getImplicitHcount

public int getImplicitHcount()

Gets the total number of implicit hydrogens attached to the molecule.

Returns:

the implicit hydrogen count or the number of query hydrogens

isMultiChiral

public boolean isMultiChiral()

Returns the multiple chirality flag. To speed up the canonical label calculations, add chirality invariant to only those molecules that has at least two possible chiral centres.

Since:

3.3

adjustMultiChiralFlag

public void adjustMultiChiralFlag()

Checks wether the molecule has multiple chiral centres

Since:

3.3