Class PharmacophoreNode


  • public class PharmacophoreNode
    extends java.lang.Object
    A PharmacophoreNode represents a node in a PharmacophoreTree. A PharmacophoreNode is associated with a list of features (hbond donor, hbond acceptor, +charge,-charge,aromatic, lipophilic) which define its chemical properties. The similarity between two pharmacophore nodes is calculated by using a combination of steric and chemical similarity.
    Author:
    joel
    • Constructor Detail

      • PharmacophoreNode

        public PharmacophoreNode​(java.util.List<java.lang.Integer> atoms,
                                 int[][] atomFunctionalities,
                                 double[] atomVolumes,
                                 int role,
                                 boolean isRing,
                                 boolean isAromatic)
      • PharmacophoreNode

        public PharmacophoreNode​(java.util.List<java.lang.Integer> atoms,
                                 int[] functionalities,
                                 java.util.List<java.lang.Double> volumes,
                                 java.util.List<java.lang.Double> weights,
                                 int role)
      • PharmacophoreNode

        public PharmacophoreNode​(java.util.List<java.lang.Integer> atoms,
                                 int[][] atomFunctionalities,
                                 double[] atomVolumes,
                                 boolean isRing,
                                 boolean isAromatic)
    • Method Detail

      • updateWeights

        public void updateWeights​(java.util.Map<java.lang.Integer,​java.util.List<java.lang.Integer>> atomToNodes)
      • calculate

        public void calculate()
        calculates the total volume and size of the node from its elements
      • calcFeatureSim

        public static double calcFeatureSim​(int[] features1,
                                            int[] features2)
      • getSimilarity

        public static double getSimilarity​(java.util.Collection<java.lang.Integer> nodes1,
                                           java.util.Collection<java.lang.Integer> nodes2,
                                           java.util.List<PharmacophoreNode> allNodes1,
                                           java.util.List<PharmacophoreNode> allNodes2)
      • getAtoms

        public java.util.List<java.lang.Integer> getAtoms()
      • getWeights

        public java.util.List<java.lang.Double> getWeights()
      • getFunctionalities

        public int[] getFunctionalities()
      • getVolumes

        public java.util.List<java.lang.Double> getVolumes()
      • getSize

        public double getSize()
      • setFunctionalities

        public void setFunctionalities​(int[] functionalities)
      • setVolumes

        public void setVolumes​(java.util.List<java.lang.Double> volumes)
      • setWeights

        public void setWeights​(java.util.List<java.lang.Double> weights)
      • setAtoms

        public void setAtoms​(java.util.List<java.lang.Integer> atoms)
      • setRole

        public void setRole​(int role)
      • isLinkNode

        public boolean isLinkNode()
      • isRing

        public boolean isRing()
      • setRing

        public void setRing​(boolean isRing)
      • isAromatic

        public boolean isAromatic()
      • setAromatic

        public void setAromatic​(boolean isAromatic)