Class ConformationRule

    • Field Detail

      • RULE_NAME

        public static final java.lang.String[] RULE_NAME
      • mAtom

        protected int[] mAtom
      • mIsEnabled

        protected boolean mIsEnabled
    • Constructor Detail

      • ConformationRule

        public ConformationRule​(int[] atom)
    • Method Detail

      • isEnabled

        public boolean isEnabled()
      • setEnabled

        public void setEnabled​(boolean b)
      • apply

        public abstract boolean apply​(Conformer conformer,
                                      double cycleFactor)
      • addStrain

        public abstract double addStrain​(Conformer conformer,
                                         double[] atomStrain)
      • getRuleType

        public abstract int getRuleType()
      • toString

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

        protected int[] getAtomList()
      • addAtomList

        protected void addAtomList​(java.lang.StringBuilder sb)
      • moveGroup

        protected void moveGroup​(Conformer conformer,
                                 int atom,
                                 int[] notList,
                                 double dx,
                                 double dy,
                                 double dz)
        Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.
        Parameters:
        conformer -
        atom -
        notList - atom list that are not moved
        dx -
        dy -
        dz -
      • moveSubstituent

        protected void moveSubstituent​(Conformer conformer,
                                       int rootAtom,
                                       int firstAtom,
                                       double dx,
                                       double dy,
                                       double dz)
        Moves all atoms of the substituent connected to rootAtom starting with firstAtom.
        Parameters:
        conformer -
        rootAtom -
        firstAtom -
        dx -
        dy -
        dz -
      • moveAtomWithUnboundedNeighbors

        protected void moveAtomWithUnboundedNeighbors​(Conformer conformer,
                                                      int atom,
                                                      double dx,
                                                      double dy,
                                                      double dz)
      • rotateAtom

        protected void rotateAtom​(Conformer conformer,
                                  int atom,
                                  int refAtom,
                                  Coordinates unit,
                                  double theta)