Class CDKRMapHandler

java.lang.Object
org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler

@Deprecated public class CDKRMapHandler extends Object
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
This algorithm derives from the algorithm described in [Tonnelier, C. and Jauffret, Ph. and Hanser, Th. and Jauffret, Ph. and Kaufmann, G., Machine Learning of generic reactions: 3. An efficient algorithm for maximal common substructure determination, Tetrahedron Comput. Methodol., 1990, 3:351-358] and modified in the thesis of T. Hanser [Unknown BibTeXML type: HAN93].
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • CDKRMapHandler

      public CDKRMapHandler()
      Deprecated.
  • Method Details

    • getSource

      public IAtomContainer getSource()
      Deprecated.
      Returns source molecule
      Returns:
      the source
    • setSource

      public void setSource(IAtomContainer aSource)
      Deprecated.
      Set source molecule
      Parameters:
      aSource - the source to set
    • getTarget

      public IAtomContainer getTarget()
      Deprecated.
      Returns target molecule
      Returns:
      the target
    • setTarget

      public void setTarget(IAtomContainer aTarget)
      Deprecated.
      Set target molecule
      Parameters:
      aTarget - the target to set
    • calculateOverlapsAndReduce

      public void calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      This function calculates all the possible combinations of MCS
      Parameters:
      molecule1 -
      molecule2 -
      shouldMatchBonds -
      Throws:
      CDKException
    • calculateOverlapsAndReduceExactMatch

      public void calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
      Parameters:
      molecule1 -
      molecule2 -
      shouldMatchBonds -
      Throws:
      CDKException
    • calculateSubGraphs

      public void calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
      Parameters:
      molecule1 -
      molecule2 -
      shouldMatchBonds -
      Throws:
      CDKException
    • calculateIsomorphs

      public void calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) throws CDKException
      Deprecated.
      This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
      Parameters:
      molecule1 -
      molecule2 -
      shouldMatchBonds -
      Throws:
      CDKException
    • removeSubGraph

      protected List<List<CDKRMap>> removeSubGraph(List<List<CDKRMap>> overlaps)
      Deprecated.
      Parameters:
      overlaps -
      Returns:
    • removeRedundantMappingsForSingleAtomCase

      protected List<CDKRMap> removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)
      Deprecated.
      Parameters:
      overlaps -
      Returns:
    • getMaximum

      protected List getMaximum(List overlaps)
      Deprecated.
      Parameters:
      overlaps -
      Returns:
    • getAllMaximum

      protected Stack<List<CDKRMap>> getAllMaximum(List<List<CDKRMap>> overlaps)
      Deprecated.
      Parameters:
      overlaps -
      Returns:
    • identifyMatchedParts

      protected void identifyMatchedParts(List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target)
      Deprecated.
      Parameters:
      list -
      source -
      target -
    • identifySingleAtomsMatchedParts

      protected void identifySingleAtomsMatchedParts(List<CDKRMap> list, IAtomContainer source, IAtomContainer target)
      Deprecated.
      Parameters:
      list -
      source -
      target -
    • isSubgraph

      protected boolean isSubgraph(List<CDKRMap> rmaps1, List<CDKRMap> rmaps2)
      Deprecated.
      Parameters:
      rmaps1 -
      rmaps2 -
      Returns:
    • isSameRMap

      protected boolean isSameRMap(CDKRMap sourceRMap, CDKRMap targetRMap)
      Deprecated.
      Parameters:
      sourceRMap - sourceAtom
      targetRMap - targetAtom
      Returns:
    • getMappings

      public List<Map<Integer,Integer>> getMappings()
      Deprecated.
      Returns mapping solutions
      Returns:
      the mappings
    • setMappings

      public void setMappings(List<Map<Integer,Integer>> mappings)
      Deprecated.
      Set mapping solutions
      Parameters:
      mappings - the mappings to set
    • isTimeoutFlag

      public boolean isTimeoutFlag()
      Deprecated.
      Returns true if a time out occurred else false
      Returns:
      the timeoutFlag
    • setTimeoutFlag

      public void setTimeoutFlag(boolean timeoutFlag)
      Deprecated.
      Set time out flag
      Parameters:
      timeoutFlag - the timeoutFlag to set