Class JarvisPatrick


  • @PublicAPI
    public class JarvisPatrick
    extends NearestNeighbors
    Performs variable-length Jarvis-Patrick clustering based on binary fingerprints (bits strings) and/or other data stored in a database table or a file. It can also be used for calculating diversity measures, like average and minimum dissimilarity of a compound library.
    This class can be used from command-line or from the API.
    See the documentation for details.

    An example for running JarvisPatrick:

     ConnectionHandler ch;
     String selectString;
     ...
     JarvisPatrick jp=new JarvisPatrick();
     jp.setInput(ch, selectString ); 
     jp.setOutput(System.out);
     jp.setDimensions(0);
     jp.setFpSize(512);
     jp.setStatNeeded(true);
     jp.setOnlyStat(false);
     jp.setStatStream(System.out);
     jp.setIdGeneration(true);
     jp.setThreshold(0.1f);
     jp.setCentralShown(true);
     jp.setMinCommonRatio(0.1f);
     jp.setSingletonNegative(true);
     jp.run();
     

    Since:
    JChem 1.6.2
    • Constructor Detail

      • JarvisPatrick

        public JarvisPatrick()
    • Method Detail

      • setMinCommonRatio

        public void setMinCommonRatio​(float ratio)
        Sets the minimum ratio of common neighbors of two compounds.
        Parameters:
        ratio - the ratio to be set
        Since:
        JChem 1.6.2
      • getMinCommonRatio

        public float getMinCommonRatio()
        Gets the minimum ratio of common neighbors of two compounds.
        Returns:
        the ratio
        Since:
        JChem 1.6.2
      • setSingletonNegative

        public void setSingletonNegative​(boolean b)
        Specifies whether singletons get negative cluste id-s.
        Parameters:
        b - If set to true, singeltons get negative cluster id-s.
        Since:
        JChem 1.6.2
      • isSingletonNegative

        public boolean isSingletonNegative()
        Indicates whether singeltons get negative cluster id-s.
        Returns:
        true, if singeltons get negative cluster id-s.
        Since:
        JChem 1.6.2
      • setCentralShown

        public void setCentralShown​(boolean b)
        Specifies if cluster centers should be diplayed.
        Parameters:
        b - if set to true, central objects are calculated and shown in output.
        Since:
        JChem 1.6.2
      • isCentralShown

        public boolean isCentralShown()
        Indicates whether central objects are displayed.
        Returns:
        true if central objects are calculated and shown in output.
        Since:
        JChem 1.6.2
      • run

        public void run()
                 throws chemaxon.clustering.ClusteringException,
                        IOException,
                        SQLException,
                        chemaxon.clustering.InvalidLicenseKeyException
        Starts processing.
        Overrides:
        run in class NearestNeighbors
        Throws:
        chemaxon.clustering.ClusteringException
        IOException
        SQLException
        chemaxon.clustering.InvalidLicenseKeyException
        Since:
        JChem 1.6.2
      • main

        public static void main​(String[] args)
        The command line version entry point. Parameter parsing, initialization then start.