Class ReactionCenterMapper


  • public class ReactionCenterMapper
    extends java.lang.Object
    This is a helper class for the RuleEnhancedMapper, which expects most of a reaction's atoms to be already mapped using an MCS or similarity guided graph-matching approach. This class tries all permutations of unmapped reactant and product atoms provided their atomic numbers and atom masses match. All solutions are scored considering bonds changed and the best scoring solution is added to the mapping number arrays. This class assumes a stoichiometrical reaction and, thus, always the same number of unmapped reactant atoms and products atoms in the same atom class.
    • Constructor Detail

      • ReactionCenterMapper

        public ReactionCenterMapper​(StereoMolecule reactant,
                                    StereoMolecule product,
                                    int[] reactantMapNo,
                                    int[] productMapNo,
                                    int mapNo)
    • Method Detail

      • completeAndScoreMapping

        public float completeAndScoreMapping()
        Tries and scores all possible mapping permutations for all of hitherto unmapped atoms. The best scoring combination is kept and its score returned. If there are no unmapped atoms, then the score of the current mapping is returned.
      • getMappedAtomCount

        public int getMappedAtomCount()