Class RigidFragment


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

      • RigidFragment

        public RigidFragment​(int coreAtomCount,
                             int[] coreToFragmentAtom,
                             int[] fragmentToOriginalAtom,
                             int[] extendedToFragmentAtom,
                             int[] originalToExtendedAtom,
                             Conformer[] conformerList,
                             double[] conformerLikelyhood)
    • Method Detail

      • getCoreCoordinates

        public Coordinates getCoreCoordinates​(int conformer,
                                              int atom)
      • getExtendedCoordinates

        public Coordinates getExtendedCoordinates​(int conformer,
                                                  int atom)
      • getConformerCount

        public int getConformerCount()
      • getConformerLikelihood

        public double getConformerLikelihood​(int i)
      • getLikelyRandomConformerIndex

        public int getLikelyRandomConformerIndex​(double random,
                                                 double progress)
        Calculates a random conformer index giving conformers with lower strains a higher chance to be selected. With a progress value of 0.0 selection likelyhoods are proportional to conformer likelyhoods due to lower strains. With increasing progress value the higher frequent conformers get less and less preferred until 1.0 without any preference.
        Parameters:
        random -
        progress - 0...1
      • originalToExtendedAtom

        public int originalToExtendedAtom​(int originalAtom)
      • coreToOriginalAtom

        public int coreToOriginalAtom​(int atom)
      • extendedToOriginalAtom

        public int extendedToOriginalAtom​(int atom)
      • getConnectionPointCount

        public int getConnectionPointCount()
      • getCoreSize

        public int getCoreSize()
        Returns:
        count of core atoms, i.e. atoms inside of rotatable bonds
      • getExtendedSize

        public int getExtendedSize()
        Returns:
        count of core and 1st shell atoms, i.e. core and rotatable bond atoms