Class 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 Detail

      • 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 Detail

      • 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