org.openscience.cdk.graph.invariant

Class EquivalentClassPartitioner

java.lang.Object

org.openscience.cdk.graph.invariant.EquivalentClassPartitioner

public class EquivalentClassPartitioner
extends Object

An algorithm for topological symmetry. This algorithm derived from the algorithm (Hu, C.Y. and Xu, L.. Analytical Chimica Acta. 1994. 295).

Author:

Junfeng Hao, Luis F. de Figueiredo

Dictionary pointer(s):

perceiveGraphSymmetry in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:perceiveGraphSymmetry]

Source code:

master

Belongs to CDK module:

extra

Created on:

2003-09-24

Constructor Summary

Constructors

Constructor and Description
EquivalentClassPartitioner() Constructor for the TopologicalEquivalentClass object.
EquivalentClassPartitioner(IAtomContainer atomContainer) Constructor for the TopologicalEquivalentClass object.

Method Summary

Modifier and Type	Method and Description
double[][]	buildBondMatrix() Build bond matrix.
double[][]	buildNodeMatrix(double[] nodeSequence) Build node Matrix.
double[][]	buildTrialNodeMatrix(double[] weight) Build trial node Matrix.
double[]	buildWeightMatrix(double[][] nodeMatrix, double[][] bondMatrix) Build weight array for the given node matrix and bond matrix.
int	checkDiffNumber(double[] weight) Get different number of the given number.
int[]	findTopoEquivClass(double[] weight) Find the topological equivalent class for the given weight.
int[]	getEquivalentClass(double[] weight) Get the final equivalent class.
int[]	getTopoEquivClassbyHuXu(IAtomContainer atomContainer) Get the topological equivalent class of the molecule.
double[]	prepareNode(IAtomContainer atomContainer) Prepare the node identifier.

Methods inherited from class java.lang.Object

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

Constructor Detail

EquivalentClassPartitioner

public EquivalentClassPartitioner()

Constructor for the TopologicalEquivalentClass object.

EquivalentClassPartitioner

public EquivalentClassPartitioner(IAtomContainer atomContainer)

Constructor for the TopologicalEquivalentClass object.

Method Detail

getTopoEquivClassbyHuXu

public int[] getTopoEquivClassbyHuXu(IAtomContainer atomContainer)
                              throws NoSuchAtomException

Get the topological equivalent class of the molecule.

Parameters:

atomContainer - atoms and bonds of the molecule

Returns:

an array contains the automorphism partition of the molecule

Throws:

NoSuchAtomException

prepareNode

public double[] prepareNode(IAtomContainer atomContainer)

Prepare the node identifier. The purpose of this is to increase the differentiation of the nodes. Detailed information please see the corresponding literature.

Parameters:

atomContainer - atoms and bonds of the molecule

Returns:

an array of node identifier

buildNodeMatrix

public double[][] buildNodeMatrix(double[] nodeSequence)

Build node Matrix.

Parameters:

nodeSequence - an array contains node number for each atom

Returns:

node Matrix

buildTrialNodeMatrix

public double[][] buildTrialNodeMatrix(double[] weight)

Build trial node Matrix.

Parameters:

weight - an array contains the weight of atom

Returns:

trial node matrix.

buildBondMatrix

public double[][] buildBondMatrix()

Build bond matrix.

Returns:

bond matrix.

buildWeightMatrix

public double[] buildWeightMatrix(double[][] nodeMatrix,
                                  double[][] bondMatrix)

Build weight array for the given node matrix and bond matrix.

Parameters:

nodeMatrix - array contains node information

bondMatrix - array contains bond information

Returns:

weight array for the node

checkDiffNumber

public int checkDiffNumber(double[] weight)

Get different number of the given number.

Parameters:

weight - array contains weight of the nodes

Returns:

number of different weight

getEquivalentClass

public int[] getEquivalentClass(double[] weight)

Get the final equivalent class.

Parameters:

weight - array contains weight of the nodes

Returns:

an array contains the automorphism partition

findTopoEquivClass

public int[] findTopoEquivClass(double[] weight)

Find the topological equivalent class for the given weight.

Parameters:

weight - array contains weight of the nodes

Returns:

an array contains the automorphism partition