Package com.actelion.research.chem.descriptor.flexophore.completegraphmatcher

Class PPNodeSimilarity

  • All Implemented Interfaces:
    IPPNodeSimilarity
    public class PPNodeSimilarity
extends java.lang.Object
implements IPPNodeSimilarity
    PPNodeSimilarity

    Copyright: Actelion Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.

    Version:
    1.0 Jan 7, 2013 MvK Start implementation Dec 2020, MvK unskewed similarity calculation for similarity hard thresh. Node similarity is now independent from query base order.
    Author:
    Modest von Korff

    • Field Detail

      • SIMILARITY_MODE_HARD_THRESH

        public static final int SIMILARITY_MODE_HARD_THRESH
        Hard thresh means if the similarity of two atom types in a node to node comparison is below a threshold the complete node to node similarity becomes 0.
        See Also:
        Constant Field Values

      • SIMILARITY_MODE_HARD_THRESH_AVR

        public static final int SIMILARITY_MODE_HARD_THRESH_AVR
        See Also:
        Constant Field Values

      • SIMILARITY_MODE_HARD_THRESH_OPTIMISTIC

        public static final int SIMILARITY_MODE_HARD_THRESH_OPTIMISTIC
        See Also:
        Constant Field Values

      • THRESH_SIMILARITY_HARD_MATCH

        public static final double THRESH_SIMILARITY_HARD_MATCH
        Similarity value distribution of the interaction table (April 2020). First two rows bin borders. Third row counts. .900 .905 .910 .915 .920 .925 .930 .935 .940 .945 .950 .955 .960 .965 .970 .975 .980 .985 .990 .995 .905 .910 .915 .920 .925 .930 .935 .940 .945 .950 .955 .960 .965 .970 .975 .980 .985 .990 .995 1.000 191 239 202 280 213 207 193 165 229 221 157 139 131 79 74 23 17 5 2 56 A similarity thresh of 0.99 allows 58 pairwise interactions.
        See Also:
        Constant Field Values

      • HARD_MATCH_OPTIMISTIC_PERCENTILE

        public static final double HARD_MATCH_OPTIMISTIC_PERCENTILE
        See Also:
        Constant Field Values

    • Constructor Detail

      • PPNodeSimilarity

        public PPNodeSimilarity​(int versionInteractionTable,
                        int modePPNodeSimilarity)
        This constructor is used for parallel mode.

    • Method Detail

      • setThreshSimilarityHardMatch

        public void setThreshSimilarityHardMatch​(double threshSimilarityHardMatch)

      • toStringParameter

        public java.lang.String toStringParameter()

      • getInstance

        public static PPNodeSimilarity getInstance​(int versionInteractionTable,
                                           int modePPNodeSimilarity)
        Use this as constructor for serial mode.
        Returns:

      • getSimilaritySimple

        public double getSimilaritySimple​(PPNode query,
                                  PPNode base)
        Parameters:
        query -
        base -
        Returns:
        Throws:
        java.lang.Exception

      • getSimilarityHardMatchMultiplicative

        public double getSimilarityHardMatchMultiplicative​(PPNode query,
                                                   PPNode base)

      • getSimilarityList

        public java.util.List<java.lang.Double> getSimilarityList​(PPNode query,
                                                          PPNode base)

      • getSimilarityHardMatchAverage

        public double getSimilarityHardMatchAverage​(PPNode query,
                                            PPNode base)

      • getSimilarityHardMatchOptimistic

        public double getSimilarityHardMatchOptimistic​(PPNode query,
                                               PPNode base)

      • getSimilarityExtraCarbonConsideration

        public double getSimilarityExtraCarbonConsideration​(PPNode query,
                                                    PPNode base)

      • isValidType

        public boolean isValidType​(int type)