Class DistHist

  • All Implemented Interfaces:
    java.io.Serializable
    Direct Known Subclasses:
    MolDistHist, MolDistHistViz

    public class DistHist
    extends java.lang.Object
    implements java.io.Serializable
    See Also:
    Serialized Form
    • Field Detail

      • arrDistHists

        protected byte[] arrDistHists
    • Constructor Detail

      • DistHist

        public DistHist()
      • DistHist

        public DistHist​(int nPPNodes)
      • DistHist

        public DistHist​(DistHist distHist)
    • Method Detail

      • copy

        public void copy​(DistHist copy)
        Parameters:
        copy - : This object is written into copy.
      • getBonds

        public int getBonds()
      • getNumPPNodes

        public int getNumPPNodes()
        Returns:
        number of pharmacophore points.
      • getSizeBytes

        public int getSizeBytes()
      • initHistogramArray

        protected void initHistogramArray​(int nPPNodes)
      • getIndex

        public static final int getIndex​(int indexNode1,
                                         int indexNode2,
                                         int size)
        Parameters:
        indexNode1 -
        indexNode2 -
        size - number of nodes
        Returns:
      • getMinDist

        public int getMinDist​(int indexAt1,
                              int indexAt2)
      • getClusterCenter

        public java.util.List<ClusterNode> getClusterCenter​(int maxDistance)
        Calculates for nodes cluster the node with the minimum rmsd to the cluster center.
        Parameters:
        maxDistance - maximum distance that a node will become a cluster member
        Returns:
        List with cluster.
      • setDistHist

        public void setDistHist​(int indexAt1,
                                int indexAt2,
                                byte[] arrHist)
      • getDistHists

        public byte[] getDistHists()
      • setDistHists

        public void setDistHists​(byte[] arr,
                                 int size,
                                 int identifier)
        Flat copy
        Parameters:
        arr -
        size -
        identifier -
      • getDistHist

        public byte[] getDistHist​(int indexAt1,
                                  int indexAt2)
        Parameters:
        indexAt1 -
        indexAt2 -
        Returns:
        deep copy.
      • getIndexPosStartForDistHist

        public int getIndexPosStartForDistHist​(int indexAt1,
                                               int indexAt2)
      • getValueAtAbsolutePosition

        public byte getValueAtAbsolutePosition​(int indexAbsolutePosition)
      • getDistHist

        public byte[] getDistHist​(int indexAt1,
                                  int indexAt2,
                                  byte[] arr)
      • getRelMaxDistInHist

        public double getRelMaxDistInHist​(int indexAt1,
                                          int indexAt2)
        To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
        Parameters:
        indexAt1 -
        indexAt2 -
        Returns:
        relative distance 0: only the first bin is occupied, 1: the last bin is occupied.
      • getMaxDistInHist

        public double getMaxDistInHist​(int indexAt1,
                                       int indexAt2)
      • getRelMaxDistInHist

        public double getRelMaxDistInHist()
        To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM. Maximum relative distance between two nodes in the object.
        Returns:
      • toStringHistsIndexed

        public java.lang.String toStringHistsIndexed()
      • getIdentifier

        public int getIdentifier()
      • setIdentifier

        public void setIdentifier​(int identifier)