Package com.actelion.research.chem.conf

Class TorsionDescriptor

  • All Implemented Interfaces:
    java.lang.Comparable<TorsionDescriptor>
    public class TorsionDescriptor
extends java.lang.Object
implements java.lang.Comparable<TorsionDescriptor>

    • Constructor Summary

      Constructors 
      Constructor Description
      TorsionDescriptor​(float[] torsion, float[] maxTorsion)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int compareTo​(TorsionDescriptor td)
      Returns 0, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE; Returns -1 if the first non-equivalent torsion angle is smaller for this than for the passed TorsionDescriptor td.
      boolean equals​(TorsionDescriptor td)
      Returns true, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE;
      float getDissimilarity​(TorsionDescriptor td, float[] bondWeight)
      Calculates a similarity value between td and this considering individual torsion values, the importance of the rotatable bond, and the ratio of rotatable/non-rotatable bonds.
      static float[] getRotatableBondWeights​(StereoMolecule mol, int[] rotatableBond)
      The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule.
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • TorsionDescriptor

        public TorsionDescriptor​(float[] torsion,
                         float[] maxTorsion)
        Parameters:
        torsion - torsion angles of rotatable bonds from 0 to maxTorsion
        maxTorsion - maxcimum torsions of rotatable bonds defining individual symmetry dependent range

    • Method Detail

      • equals

        public boolean equals​(TorsionDescriptor td)
        Returns true, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE;
        Parameters:
        td -
        Returns:

      • compareTo

        public int compareTo​(TorsionDescriptor td)
        Returns 0, if none of the torsion angles are more different than TORSION_EQUIVALENCE_TOLERANCE; Returns -1 if the first non-equivalent torsion angle is smaller for this than for the passed TorsionDescriptor td.
        Specified by:
        compareTo in interface java.lang.Comparable<TorsionDescriptor>
        Parameters:
        td -
        Returns:

      • getRotatableBondWeights

        public static float[] getRotatableBondWeights​(StereoMolecule mol,
                                              int[] rotatableBond)
        The relevance of a rotatable bond and its torsion angle for creating substantially different conformers depends on how close the bond is to the center of the molecule. Bond relevance values range from 1.0/atomCount (e.g. bond to methyl group) to 1.0 (bond dividing molecule into two equally large parts). Ring bonds are assigned a relevance value of 0.33 independent of their location.
        Parameters:
        mol -
        rotatableBond -
        Returns:

      • getDissimilarity

        public float getDissimilarity​(TorsionDescriptor td,
                              float[] bondWeight)
        Calculates a similarity value between td and this considering individual torsion values, the importance of the rotatable bond, and the ratio of rotatable/non-rotatable bonds.
        Parameters:
        td -
        Returns:

      • toString

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