Class RootAtomPairSource


  • public class RootAtomPairSource
    extends java.lang.Object
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getManualMapCount()  
      int getMappableAtomCount()  
      boolean hasNextPairSequence()  
      com.actelion.research.chem.reaction.mapping.RootAtomPair nextPair()
      This creates and returns the next reactant/product atom pair to serve as starting point for building equivalent atom graphs that logically match reactant subgraphs to product subgraphs.
      • Methods inherited from class java.lang.Object

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

      • RootAtomPairSource

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

      • getMappableAtomCount

        public int getMappableAtomCount()
      • getManualMapCount

        public int getManualMapCount()
      • hasNextPairSequence

        public boolean hasNextPairSequence()
      • nextPair

        public com.actelion.research.chem.reaction.mapping.RootAtomPair nextPair()
        This creates and returns the next reactant/product atom pair to serve as starting point for building equivalent atom graphs that logically match reactant subgraphs to product subgraphs. The most plausible atom pair regarding reactant to product atom similarity is returned first. If multiple equi-plausible pairs exist, the permutation value passed to the constructor determines, which of the pairs is returned. Root atom pairs meet these conditions:
        - they match in terms of circular fragment on reactant and products side
        - if multiple symmetrically equivalent pairs exist, exactly one of them is marked as allowed root pair
        - each of the reactant and product atoms have at least one unmapped neighbour
        Returns:
        pair of currently obvious root atom pairs