Class McgregorHelper

java.lang.Object
org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper

@Deprecated public class McgregorHelper 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.
Helper Class for McGregor algorithm. The second part of the program extents the mapping by the McGregor algorithm in case, that not all atoms of molecule A and molecule B are mapped by the clique approach.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • McgregorHelper

      protected McgregorHelper(boolean mappingCheckFlag, int mappedAtomCount, List<Integer> mappedAtomsOrg, int neighborBondNumA, int neighborBondNumB, List<Integer> iBondNeighborAtomsA, List<Integer> iBondNeighborAtomsB, List<String> cBondNeighborsA, List<String> cBondNeighborsB, int setNumA, int setNumB, List<Integer> iBondSetA, List<Integer> iBondSetB, List<String> cBondSetA, List<String> cBondSetB)
      Deprecated.
      Stores the variables
      Parameters:
      mappingCheckFlag -
      mappedAtomCount -
      mappedAtomsOrg -
      neighborBondNumA -
      neighborBondNumB -
      iBondNeighborAtomsA -
      iBondNeighborAtomsB -
      cBondNeighborsA -
      cBondNeighborsB -
      setNumA -
      setNumB -
      iBondSetA -
      iBondSetB -
      cBondSetA -
      cBondSetB -
  • Method Details

    • getCBondSetA

      protected List<String> getCBondSetA()
      Deprecated.
      Returns:
      the cBondSetA
    • getCBondSetB

      protected List<String> getCBondSetB()
      Deprecated.
      Returns:
      the cBondSetB
    • isMappingCheckFlag

      protected boolean isMappingCheckFlag()
      Deprecated.
      Returns:
      the mappingCheckFlag
    • getMappedAtomCount

      protected int getMappedAtomCount()
      Deprecated.
      Returns:
      the mappedAtomCount
    • getMappedAtomsOrg

      protected List<Integer> getMappedAtomsOrg()
      Deprecated.
      Returns:
      the mappedAtomsOrg
    • getNeighborBondNumA

      protected int getNeighborBondNumA()
      Deprecated.
      Returns:
      the neighborBondNumA
    • getNeighborBondNumB

      protected int getNeighborBondNumB()
      Deprecated.
      Returns:
      the neighborBondNumB
    • getiBondNeighborAtomsA

      protected List<Integer> getiBondNeighborAtomsA()
      Deprecated.
      Returns:
      the iBondNeighborAtomsA
    • getiBondNeighborAtomsB

      protected List<Integer> getiBondNeighborAtomsB()
      Deprecated.
      Returns:
      the iBondNeighborAtomsB
    • getcBondNeighborsA

      protected List<String> getcBondNeighborsA()
      Deprecated.
      Returns:
      the cBondNeighborsA
    • getcBondNeighborsB

      protected List<String> getcBondNeighborsB()
      Deprecated.
      Returns:
      the cBondNeighborsB
    • getSetNumA

      protected int getSetNumA()
      Deprecated.
      Returns:
      the setNumA
    • getIBondSetA

      protected List<Integer> getIBondSetA()
      Deprecated.
      Returns:
      the iBondSetA
    • getIBondSetB

      protected List<Integer> getIBondSetB()
      Deprecated.
      Returns:
      the iBondSetB