Package 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:
main
Belongs to CDK module:
extra
Created on:
2003-09-24

  • Constructor Details

    • EquivalentClassPartitioner

      public EquivalentClassPartitioner()
      Constructor for the TopologicalEquivalentClass object.

    • EquivalentClassPartitioner

      public EquivalentClassPartitioner(IAtomContainer atomContainer)
      Constructor for the TopologicalEquivalentClass object.

  • Method Details

    • 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