Class GenerateCompatibilityGraph

java.lang.Object
org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph

@Deprecated public final class GenerateCompatibilityGraph extends Object
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
This class generates compatibility graph between query and target molecule. It also markes edges in the compatibility graph as c-edges or d-edges.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • GenerateCompatibilityGraph

      public GenerateCompatibilityGraph()
      Deprecated.
      Default constructor added
    • GenerateCompatibilityGraph

      public GenerateCompatibilityGraph(IAtomContainer source, IAtomContainer target, boolean shouldMatchBonds) throws IOException
      Deprecated.
      Generates a compatibility graph between two molecules
      Parameters:
      source -
      target -
      shouldMatchBonds -
      Throws:
      IOException
  • Method Details

    • compatibilityGraphNodes

      protected int compatibilityGraphNodes() throws IOException
      Deprecated.
      Generate Compatibility Graph Nodes
      Returns:
      Throws:
      IOException
    • compatibilityGraph

      protected int compatibilityGraph() throws IOException
      Deprecated.
      Generate Compatibility Graph Nodes Bond Insensitive
      Returns:
      Throws:
      IOException
    • compatibilityGraphNodesIfCEdgeIsZero

      protected Integer compatibilityGraphNodesIfCEdgeIsZero() throws IOException
      Deprecated.
      compGraphNodesCZero is used to build up of the edges of the compatibility graph
      Returns:
      Throws:
      IOException
    • compatibilityGraphCEdgeZero

      protected int compatibilityGraphCEdgeZero() throws IOException
      Deprecated.
      compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BIS
      Returns:
      Throws:
      IOException
    • getCEgdes

      public List<Integer> getCEgdes()
      Deprecated.
    • getDEgdes

      protected List<Integer> getDEgdes()
      Deprecated.
    • getCompGraphNodes

      protected List<Integer> getCompGraphNodes()
      Deprecated.
    • getCEdgesSize

      protected int getCEdgesSize()
      Deprecated.
    • getDEdgesSize

      protected int getDEdgesSize()
      Deprecated.
    • getCompGraphNodesCZero

      protected List<Integer> getCompGraphNodesCZero()
      Deprecated.
    • clearCEgdes

      protected void clearCEgdes()
      Deprecated.
    • clearDEgdes

      protected void clearDEgdes()
      Deprecated.
    • clearCompGraphNodes

      protected void clearCompGraphNodes()
      Deprecated.
    • clearCompGraphNodesCZero

      protected void clearCompGraphNodesCZero()
      Deprecated.
    • resetCEdgesSize

      protected void resetCEdgesSize()
      Deprecated.
    • resetDEdgesSize

      protected void resetDEdgesSize()
      Deprecated.
    • clear

      public void clear()
      Deprecated.
    • isMatchBond

      public boolean isMatchBond()
      Deprecated.
      Returns:
      the shouldMatchBonds
    • setMatchBond

      public void setMatchBond(boolean shouldMatchBonds)
      Deprecated.
      Parameters:
      shouldMatchBonds - the shouldMatchBonds to set