Class ChemStructureSimilarity


  • public class ChemStructureSimilarity
    extends java.lang.Object
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static double calculateTanimoto​(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.util.LinkedHashMap<java.lang.String,​java.lang.String> queries)  
      static double calculateTanimotoWithCustomSmarts​(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.lang.String[] smarts)  
      static double calculateTanimotoWithCustomSmartsAndCounts​(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.lang.String[] smarts)  
      static double calculateTanimotoWithMACCS​(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2)  
      static void generateCsv​(java.util.HashMap<java.lang.String,​java.lang.Double> tanimotoList, java.lang.String outputname)  
      static java.lang.String[] getSmarts()  
      static java.util.HashMap<java.lang.String,​java.lang.Double> tanimotoListCreator​(java.util.HashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainer> compounds, java.util.LinkedHashMap<java.lang.String,​java.lang.String> queries)  
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • ChemStructureSimilarity

        public ChemStructureSimilarity()
    • Method Detail

      • calculateTanimotoWithCustomSmarts

        public static double calculateTanimotoWithCustomSmarts​(org.openscience.cdk.interfaces.IAtomContainer molecule1,
                                                               org.openscience.cdk.interfaces.IAtomContainer molecule2,
                                                               java.lang.String[] smarts)
                                                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • calculateTanimotoWithCustomSmartsAndCounts

        public static double calculateTanimotoWithCustomSmartsAndCounts​(org.openscience.cdk.interfaces.IAtomContainer molecule1,
                                                                        org.openscience.cdk.interfaces.IAtomContainer molecule2,
                                                                        java.lang.String[] smarts)
                                                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • calculateTanimoto

        public static double calculateTanimoto​(org.openscience.cdk.interfaces.IAtomContainer molecule1,
                                               org.openscience.cdk.interfaces.IAtomContainer molecule2,
                                               java.util.LinkedHashMap<java.lang.String,​java.lang.String> queries)
                                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • calculateTanimotoWithMACCS

        public static double calculateTanimotoWithMACCS​(org.openscience.cdk.interfaces.IAtomContainer molecule1,
                                                        org.openscience.cdk.interfaces.IAtomContainer molecule2)
                                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getSmarts

        public static java.lang.String[] getSmarts()
                                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • tanimotoListCreator

        public static java.util.HashMap<java.lang.String,​java.lang.Double> tanimotoListCreator​(java.util.HashMap<java.lang.String,​org.openscience.cdk.interfaces.IAtomContainer> compounds,
                                                                                                     java.util.LinkedHashMap<java.lang.String,​java.lang.String> queries)
                                                                                              throws java.lang.Exception
        Throws:
        java.lang.Exception
      • generateCsv

        public static void generateCsv​(java.util.HashMap<java.lang.String,​java.lang.Double> tanimotoList,
                                       java.lang.String outputname)