Package chemaxon.util

Class HitDisplayUtil

java.lang.Object
chemaxon.util.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 Details

  • Constructor Details

    • HitDisplayUtil

      public HitDisplayUtil()

  • Method Details

    • getScaffoldOrientatedHit

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static Molecule getScaffoldOrientatedHit(Molecule query, Molecule target, int[] hit)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Use MolAligner.align(Molecule, Molecule, int[]) instead
      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

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static Molecule getScaffoldOrientatedHit(Molecule query, Molecule target, int[][] groupHit)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Use MolAligner.align(Molecule, Molecule, int[][]) instead
      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