Package chemaxon.util

Class HitDisplayUtil


  • @PublicAPI
    public class HitDisplayUtil
    extends Object
    Class providing some utility tools for displaying hit results with hit coloring, alignment, partial clean, etc.
    Since:
    Marvin 5.1
    • Field Detail

    • Constructor Detail

      • HitDisplayUtil

        public HitDisplayUtil()
    • Method Detail

      • getScaffoldOrientatedHit

        public static Molecule getScaffoldOrientatedHit​(Molecule scaffold,
                                                        Molecule molToAlign)
        Only for internal use!
        Parameters:
        scaffold - base for alignment
        molToAlign - molecule that should be aligned to scaffold
        Returns:
        aligned molecule
      • getScaffoldOrientatedHit

        public static Molecule getScaffoldOrientatedHit​(Molecule query,
                                                        Molecule target,
                                                        int[] hit)
        Returns an aligned (rotated) version of molToAlign that contains scaffold - possibly in the same position or optimally close to it.
        Parameters:
        query - scaffold baseline for alignment
        target - molToAlign molecule that should be aligned to scaffold
        hit - ordered array (its size must be equal to scaffold size), describes matchings between scaffold and molToAlign atom indices (e.g. scaffold[2] --> molToAlign[5] ==> hit[2] = 5)
        Returns:
        aligned molecule
      • getScaffoldOrientatedHit

        public static Molecule getScaffoldOrientatedHit​(Molecule query,
                                                        Molecule target,
                                                        int[][] groupHit)
        Returns an aligned (rotated) version of molToAlign that contains scaffold - possibly in the same position or optimally close to it.
        Parameters:
        query - scaffold baseline for alignment
        target - molToAlign molecule that should be aligned to scaffold
        groupHit - a map of the atom ids in the query and the target returned by a search. Its size must be equal to scaffold size.
        Returns:
        aligned molecule
      • colorHit

        public static Molecule colorHit​(Molecule substructure,
                                        Molecule target,
                                        int[] hit,
                                        HitColoringAndAlignmentOptions options)
        Returns the colored copy of the specified target structure, the original target is kept unchanged.
        Parameters:
        substructure - the structure taken as a template for coloring
        target - the structure whose colored copy is returned
        hit - maps atoms of the template to atoms in the colored structure
        options - coloring options
        Returns:
        the colored molecule
      • color

        public static void color​(Molecule substructure,
                                 Molecule molToColor,
                                 HitColoringAndAlignmentOptions options)
        Performs hit coloring on the specified structure. Only for internal use!
        Parameters:
        substructure - the structure taken as a template for coloring
        molToColor - the structure to be colored
        options - coloring options
      • color

        public static void color​(Molecule query,
                                 Molecule target,
                                 int[] hit,
                                 HitColoringAndAlignmentOptions options)
        Performs hit coloring on the specified structure. Only for internal use!
        Parameters:
        query - the query structure (template for coloring)
        target - the target structure to be colored
        hit - maps atoms of the template to atoms in the colored structure. This array can be an extended single hit.
        options - coloring options