Class PharmacophoreTreeGenerator


  • public class PharmacophoreTreeGenerator
    extends java.lang.Object
    Generates a PharmacophoreTree from a StereoMolecule. Calculates chemical features and steric properties of the nodes spanning the tree. Cycles are resolved by merging nodes and introducing zero-nodes.
    Author:
    joel
    • Field Detail

      • RGROUPS

        public static final java.util.Set<java.lang.String> RGROUPS
    • Method Detail

      • generate

        public static PharmacophoreTree generate​(StereoMolecule mol,
                                                 java.util.Map<java.lang.Integer,​java.util.List<java.lang.Integer>> atomToNodes,
                                                 java.util.List<java.util.Set<java.lang.Integer>> rings)
        the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they react
        Parameters:
        mol -
        atomToNodes -
        rings -
        Returns:
      • addNode

        public static void addNode​(PharmacophoreNode node,
                                   java.util.List<PharmacophoreNode> nodes,
                                   java.util.Map<java.lang.Integer,​java.util.List<java.lang.Integer>> atomToNodes)
      • getSmallestRingsOfAtom

        public static java.util.List<java.lang.Integer> getSmallestRingsOfAtom​(RingCollection rc,
                                                                               int atom)
      • getAtomVolumes

        public static double[] getAtomVolumes​(StereoMolecule mol)