Class SSSearcherWithIndex


  • public class SSSearcherWithIndex
    extends java.lang.Object
    • Field Detail

      • cKeyIDCode

        public static final java.lang.String[] cKeyIDCode
    • Constructor Detail

      • SSSearcherWithIndex

        public SSSearcherWithIndex()
      • SSSearcherWithIndex

        public SSSearcherWithIndex​(int matchMode)
    • Method Detail

      • getNoOfKeys

        public static int getNoOfKeys()
      • getKeyFragment

        public static StereoMolecule getKeyFragment​(int no)
      • setFragment

        @Deprecated
        public void setFragment​(StereoMolecule fragment,
                                int[] index)
        Deprecated.
      • setFragment

        @Deprecated
        public void setFragment​(java.lang.String idcode,
                                int[] index)
        Deprecated.
      • setFragment

        @Deprecated
        public void setFragment​(byte[] idcode,
                                int[] index)
        Deprecated.
      • setMolecule

        @Deprecated
        public void setMolecule​(StereoMolecule molecule,
                                int[] index)
        Deprecated.
      • setMolecule

        @Deprecated
        public void setMolecule​(java.lang.String idcode,
                                int[] index)
        Deprecated.
      • setMolecule

        @Deprecated
        public void setMolecule​(byte[] idcode,
                                int[] index)
        Deprecated.
      • setFragment

        public void setFragment​(StereoMolecule fragment,
                                long[] index)
      • setFragment

        public void setFragment​(java.lang.String idcode,
                                long[] index)
      • setFragment

        public void setFragment​(byte[] idcode,
                                long[] index)
      • setMolecule

        public void setMolecule​(StereoMolecule molecule,
                                long[] index)
      • setMolecule

        public void setMolecule​(java.lang.String idcode,
                                long[] index)
      • setMolecule

        public void setMolecule​(byte[] idcode,
                                long[] index)
      • getFirstHittingLongIndexBlockNo

        public int getFirstHittingLongIndexBlockNo()
      • getMolecule

        public StereoMolecule getMolecule()
        Returns the most recently defined molecule. If the molecule was passed as idcode and was not created yet, then a molecule is constructed from the idcode and returned.
        Returns:
        current Molecule (null, if setMolecule() has never been called)
      • isFragmentIndexInMoleculeIndex

        public boolean isFragmentIndexInMoleculeIndex()
        Returns:
        whether the fragment fingerprint bits are all present in the molecule bits
      • isFragmentInMoleculeWithoutIndex

        public boolean isFragmentInMoleculeWithoutIndex()
      • findFragmentInMoleculeWithoutIndex

        public int findFragmentInMoleculeWithoutIndex​(int countMode)
      • isFragmentInMolecule

        public boolean isFragmentInMolecule()
      • findFragmentInMolecule

        public int findFragmentInMolecule()
      • findFragmentInMolecule

        public int findFragmentInMolecule​(int countMode,
                                          int matchMode)
      • findFragmentInMolecule

        public int findFragmentInMolecule​(int countMode,
                                          int matchMode,
                                          boolean[] atomExcluded)
      • getMatchList

        public java.util.ArrayList<int[]> getMatchList()
        If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e. int arrays mapping fragment atoms to molecule atoms. Atoms being part of a matched bridge bond are naturally not covered by the mapping.
        Note: If some query fragment atoms are marked as exclude group, then the respective matchlist values are -1.
        Returns:
        list of distinct counted matches.
      • createLongIndex

        public long[] createLongIndex​(StereoMolecule mol)
      • getSimilarityTanimoto

        public static float getSimilarityTanimoto​(int[] index1,
                                                  int[] index2)
      • getSimilarityTanimoto

        public static float getSimilarityTanimoto​(long[] index1,
                                                  long[] index2)
      • getSimilarityAngleCosine

        public static float getSimilarityAngleCosine​(int[] index1,
                                                     int[] index2)
      • getIndexFromHexString

        public static int[] getIndexFromHexString​(java.lang.String hex)
      • getIndexFromHexString

        public static int[] getIndexFromHexString​(byte[] bytes)
      • getLongIndexFromHexString

        public static long[] getLongIndexFromHexString​(java.lang.String hex)
      • getLongIndexFromHexString

        public static long[] getLongIndexFromHexString​(byte[] bytes)
      • getHexStringFromIndex

        public static java.lang.String getHexStringFromIndex​(int[] index)
      • stop

        public void stop()