Class BondRotationHelper


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

      • BondRotationHelper

        public BondRotationHelper​(StereoMolecule mol)
      • BondRotationHelper

        public BondRotationHelper​(StereoMolecule mol,
                                  boolean includeTerminalPolarH)
    • Method Detail

      • initialize

        public void initialize()
      • predictAtomSequence

        public static void predictAtomSequence​(StereoMolecule mol,
                                               int bond,
                                               int[] torsionAtoms,
                                               int[] rearAtoms)
      • isRotatableBond

        public boolean isRotatableBond​(int bond)
      • getRotatableBonds

        public int[] getRotatableBonds()
      • rotateSmallerSide

        public void rotateSmallerSide​(int bond,
                                      double alpha)
      • rotateAroundBond

        public void rotateAroundBond​(int bondIndex,
                                     double alpha,
                                     Conformer conf,
                                     boolean biggerSide)
        rotate torsion angle of a conformer
        Parameters:
        bond -
        alpha -
        conf -
      • setRotatableBonds

        public void setRotatableBonds​(int[] rotatableBonds)
      • getSmallerSideAtomLists

        public int[][] getSmallerSideAtomLists()
      • setSmallerSideAtomLists

        public void setSmallerSideAtomLists​(int[][] smallerSideAtomLists)
      • getTorsionAtoms

        public int[][] getTorsionAtoms()
      • setTorsionAtoms

        public void setTorsionAtoms​(int[][] torsionAtoms)
      • getRearAtoms

        public int[][] getRearAtoms()
      • setRearAtoms

        public void setRearAtoms​(int[][] rearAtoms)
      • getRotationCenters

        public int[] getRotationCenters()
      • setRotationCenters

        public void setRotationCenters​(int[] rotationCenters)
      • getTorsionIDs

        public java.lang.String[] getTorsionIDs()
      • setTorsionIDs

        public void setTorsionIDs​(java.lang.String[] torsionIDs)