Class MCS


  • public class MCS
    extends java.lang.Object
    • Constructor Detail

      • MCS

        public MCS()
      • MCS

        public MCS​(int ringStatus)
      • MCS

        public MCS​(int ringStatus,
                   SSSearcher searcher)
    • Method Detail

      • setSSSearcher

        public void setSSSearcher​(SSSearcher sss)
      • set

        public void set​(StereoMolecule mol,
                        StereoMolecule frag)
        mol should contain equal or more bonds than frag.
        Parameters:
        mol -
        frag -
      • set

        public void set​(StereoMolecule mol,
                        StereoMolecule frag,
                        boolean[] excluded)
        mol should contain equal or more bonds than frag. If frag contains more than one molecule only the biggest one is considered.
        Parameters:
        mol -
        frag -
        excluded -
      • getAllCommonSubstructures

        public java.util.LinkedList<StereoMolecule> getAllCommonSubstructures()
        All molecules which are sub structures of an other molecule in the list are removed.
        Returns:
      • getMCS

        public StereoMolecule getMCS()
        Returns:
        maximum common substructure at top of list or null of none common MCS was found.
      • getMCSBondArray

        public boolean[][] getMCSBondArray​(boolean[] arrBondMCSMol,
                                           boolean[] arrBondFrag)
        Calculates the bond arrays for molecule and fragment for their maximum common substructure.
        Parameters:
        arrBondMCSMol - result array. Null or initialized with the length number of bonds in molecule.
        arrBondFrag - result array. Null or initialized with the length number of bonds in fragment.
        Returns:
        two arrays, in the first array the bits are set 'true' which corresponds to the bonds for maximum common substructure in the molecule. In the second are the bits set 'true' which corresponds to the bonds for maximum common substructure in the fragment.
      • getArrMatchListFrag2Mol

        public int[] getArrMatchListFrag2Mol()
        delivers the match list indices from getMCSBondArray(...) index is the Fragment atom index, value is the matched atom index in molecule.
        Returns:
        null if no match was found.
      • getScore

        public double getScore()
        Calculates the score by bonds_mcs/Max(bonds_mol, bonds_frag)
        Returns:
        1 if full overlap and 0 if no overlap at all.
      • isConsiderAromaticRings

        public boolean isConsiderAromaticRings()
      • isConsiderRings

        public boolean isConsiderRings()