Package chemaxon.clustering

Class JarvisPatrick

java.lang.Object
chemaxon.clustering.Common
chemaxon.clustering.NearestNeighbors
chemaxon.clustering.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 Details

    • JarvisPatrick

      public JarvisPatrick()

  • Method Details

    • 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 ClusteringException, IOException, SQLException, InvalidLicenseKeyException
      Starts processing.
      Overrides:
      run in class NearestNeighbors
      Throws:
      ClusteringException
      IOException
      SQLException
      InvalidLicenseKeyException
      Since:
      JChem 1.6.2

    • main

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JAN_01_2025) public static void main(String[] args)
      Deprecated, for removal: This API element is subject to removal in a future version.
      This main method will be removed, CLI interfaces should not be used directly from Java code.
      The command line version entry point. Parameter parsing, initialization then start.