Class MappingScorer


  • public class MappingScorer
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      MappingScorer​(StereoMolecule reactant, StereoMolecule product)
      Instantiates a mapping scorer that judges the quality of a mapping by adding penalties for every bond being broken, created, or changed.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int[] createReactantToProductAtomMap​(int[] reactantMapNo, int[] productMapNo)  
      float scoreMapping​(int[] reactantToProductAtom)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • MappingScorer

        public MappingScorer​(StereoMolecule reactant,
                             StereoMolecule product)
        Instantiates a mapping scorer that judges the quality of a mapping by adding penalties for every bond being broken, created, or changed. In principle the panelty for any created or broken bond is 2.0, and for any changed bond order is 1.0. A change from/to delocalized to/from single or double is considered a change. Broken or created bonds at typical break locations, e.g. ester cleavage, get slightly lower penalties than 2.0. Changes of implicit hydrogen counts contribute with a factor of 2.0.
        Parameters:
        reactant -
        product -
    • Method Detail

      • createReactantToProductAtomMap

        public int[] createReactantToProductAtomMap​(int[] reactantMapNo,
                                                    int[] productMapNo)
      • scoreMapping

        public float scoreMapping​(int[] reactantToProductAtom)
        Parameters:
        reactantToProductAtom -
        Returns:
        the mapping score considering all (score is negative value; 0: no bond changes)