Class SubGraphIndices


  • public class SubGraphIndices
    extends java.lang.Object
    SubGraphIndices A class to handle indices in a molecular graph. It is just a hash set for integer with some methods.

    Copyright: Actelion Pharmaceuticals Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.

    Created by korffmo1 on 23.02.16.
    • Constructor Detail

      • SubGraphIndices

        public SubGraphIndices()
    • Method Detail

      • getNumIndices

        public int getNumIndices()
      • clear

        public void clear()
      • addIndex

        public void addIndex​(int indexAtom)
      • addIndex

        public void addIndex​(int[] arrIndexAtom)
      • getAtomIndices

        public int[] getAtomIndices()
      • contains

        public boolean contains​(int indexAtom)
      • equals

        public boolean equals​(java.lang.Object obj)
        Overrides:
        equals in class java.lang.Object
      • getNumOverlappingIndices

        public int getNumOverlappingIndices​(SubGraphIndices frag)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • merge

        public static void merge​(java.util.List<SubGraphIndices> liFragment)
        Merges fragments containing a common atom index. The fragments in the list are merged and the list is shrinked.
        Parameters:
        liFragment -
      • mergeOverlapping

        public static java.util.List<SubGraphIndices> mergeOverlapping​(java.util.List<SubGraphIndices> liFragment,
                                                                       int minNumIndicesOverlapping)
        Merges overlapping fragments. They may share a minimum number of overlapping indices.
        Parameters:
        liFragment -
        minNumIndicesOverlapping -
        Returns:
      • addAtomIndices

        protected static void addAtomIndices​(HashSetInt hs,
                                             java.util.List<SubGraphIndices> liFragment)
        Adds the atom indices to the hash set.
        Parameters:
        hs -
        liFragment -
      • getComparatorNumIndices

        public static java.util.Comparator<SubGraphIndices> getComparatorNumIndices()