Class Decomposition

    • Constructor Detail

      • Decomposition

        protected Decomposition​(Molecule query,
                                Molecule target,
                                int[][] groupHit,
                                Molecule[] ligands,
                                Molecule scaffold)
        Constructor.
        Parameters:
        query - the R-grouped query
        target - the target
        groupHit - the group hit
        ligands - the R-ligands
        scaffold - the scaffold
    • Method Detail

      • equals

        public boolean equals​(Object o)
        Returns true if this decomposition is equivalent to the specified decomposition. Equivalent decompositions correspond to the same query and target and provide equivalent scaffold and R-ligands.
        Overrides:
        equals in class Object
        Parameters:
        o - the other decomposition
        Returns:
        true if this decomposition is equivalent to the other decomposition
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object
      • getQuery

        public Molecule getQuery()
        Returns the R-grouped query used in the R-group decomposition.
        Returns:
        the R-grouped query.
      • getTarget

        public Molecule getTarget()
        Returns the target.
        Returns:
        the target
      • getGroupHit

        public int[][] getGroupHit()
        Returns the group hit corresponding to the R-group decomposition. The group hit assigns the matching target index array for each query atom index. Negative entries refer to implicit H matches or specific constants, see Search.findNext() for a detailed description.
        Returns:
        the group hit corresponding to the R-group decomposition
      • getLigands

        public Molecule[] getLigands()
        Returns the R-ligand array. This array maps query atom indexes to the corresponding R-ligand molecules for undefined R-atoms and assigns null to other query atoms.
        Returns:
        the R-ligand array
      • getScaffold

        public Molecule getScaffold()
        Returns the scaffold in target.
        Returns:
        the scaffold
      • getLigandIds

        public int[] getLigandIds()
        Returns the target ligand IDs. This is a map of target atoms:
        • -2 for atoms outside the group hit
        • -1 for scaffold atoms
        • least corresponding query R-atom index for R-ligands
        Returns:
        the target ligand IDs
      • color

        public void color()
        Colors ligands, scaffold, query and target by setting color data in atoms by calling MolAtom.setSetSeq(int). This coloring method can be used with MRV output. The atom set values are the following:
        • 1 for scaffold atoms
        • R-atom ID + 1 for query R-atoms and target R-ligands (in case of R-bridging the R-atom with least query atom index is used)
        • 0 for target atoms falling outside the decomposition (unmapped fragments)
        See Also:
        color(java.lang.String)
      • color

        public static void color​(Molecule mol)
        Colors a molecule by setting color data in atoms by calling MolAtom.setSetSeq(int). This coloring method can be used with MRV output. The atom set values are the following:
        • 1 for scaffold atoms
        • R-atom ID + 1 for query R-atoms and target R-ligands (in case of R-bridging the R-atom with least query atom index is used)
        Parameters:
        mol - the input/output molecule
      • color

        public void color​(String colorTag)
        Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag). This coloring method can be used with both SDF and MRV output. The color data is a ';'-separated string of atom symbols in atom index order. The symbols are the following:
        • 0 for scaffold atoms
        • the corresponding query R-atom ID (in case of R-bridging the R-atom with least query atom index is used)
        • - for others
        The colored molecules are seen in MView with the following parametrization:
         mview -t DMAP -p Colors.ini mols.sdf
         
        where DMAP is the color SDF tag, Colors.ini is the coloring configuration file containing symbol - color pairs, e.g.:
         0=red
         -=black
         1=green
         2=blue
         3=orange
         4=fuchsia
         empty=black
         other=gray
         
        Parameters:
        colorTag - the property name (SDF tag) storing the color data
        See Also:
        color()
      • color

        public static void color​(Molecule mol,
                                 String colorTag)
        Colors a molecule by setting color data in the specified molecule property (SDF tag). This coloring method can be used with both SDF and MRV output. The color data is a ';'-separated string of atom symbols in atom index order. The symbols are the following:
        • 0 for scaffold atoms
        • the corresponding query R-atom ID (in case of R-bridging the R-atom with least query atom index is used)
        The colored molecules are seen in MView with the following parametrization:
         mview -t DMAP -p Colors.ini mols.sdf
         
        where DMAP is the color SDF tag, Colors.ini is the coloring configuration file containing symbol - color pairs, e.g.:
         0=red
         -=black
         1=green
         2=blue
         3=orange
         4=fuchsia
         empty=black
         other=gray
         
        Parameters:
        mol - the input/output molecule to be colored
        colorTag - the property name (SDF tag) storing the color data