Class SelfOrganizedConformer

  • All Implemented Interfaces:
    java.lang.Comparable<Conformer>

    public class SelfOrganizedConformer
    extends Conformer
    • Constructor Detail

      • SelfOrganizedConformer

        public SelfOrganizedConformer​(StereoMolecule mol)
    • Method Detail

      • isWorseThan

        public boolean isWorseThan​(SelfOrganizedConformer conformer)
        Checks whether the total strain of this Conformer is larger than that of conformer, assuming that the calculated strain values are up-to-date.
        Parameters:
        conformer -
        Returns:
      • calculateStrain

        public void calculateStrain​(java.util.ArrayList<ConformationRule> ruleList)
      • getAtomStrain

        public double getAtomStrain​(int atom)
      • getRuleStrain

        public double getRuleStrain​(int rule)
      • getHighestAtomStrain

        public double getHighestAtomStrain()
      • getTotalStrain

        public double getTotalStrain()
      • getLikelyhood

        public double getLikelyhood()
        Tries to estimate the relative likelyhood of this conformer from atom strains considering an unstrained conformer to have a likelyhood of 1.0.
        Returns:
        conformer likelyhood
      • isAcceptable

        protected boolean isAcceptable​(java.util.ArrayList<ConformationRule> ruleList)
        Parameters:
        ruleList - may be null, if isAcceptable() was called earlier and neither ruleList not conformer were changes since
        Returns:
      • invalidateStrain

        public void invalidateStrain()
      • calculateDescriptor

        public void calculateDescriptor​(int[] rotatableBond)
        Calculates the torsion descriptor for the current coordinates. Use calculateRotatableBondsForDescriptor() once and pass it for every new conformer to this method.
        Parameters:
        rotatableBond - set of rotatable bonds to be considered
      • equals

        public boolean equals​(SelfOrganizedConformer conformer)
        Returns true, if none of the torsion angles between both conformers are more different than TorsionDescriptor.TORSION_EQUIVALENCE_TOLERANCE; Calling this method requires that calculateDescriptor() has been called earlier.
        Parameters:
        conformer -
        Returns:
        true if all torsions are similar
      • isUsed

        public boolean isUsed()
      • setUsed

        public void setUsed​(boolean isUsed)