chemaxon.util
Class HitDisplayUtil

java.lang.Object
  chemaxon.util.HitDisplayUtil

public class HitDisplayUtil
extends java.lang.Object

Class providing some utility tools for displaying hit results with hit coloring, alignment, partial clean, etc.

Since:

Marvin 5.1

Author:

Szilard Dorant, Tamas Csizmazia

Constructor Summary

HitDisplayUtil()

Method Summary

static void	color(Molecule substructure, Molecule molToColor, HitColoringAndAlignmentOptions options) Performs hit coloring on the specified structure
static void	color(Molecule substructure, Molecule molToColor, int[] hit, HitColoringAndAlignmentOptions options) Performs hit coloring on the specified structure
protected static java.util.ArrayList	getNonHitBonds(Molecule query, Molecule target, int[] hit) Returns the bonds of the target molecule that should not be colored in hit highlighting.
static Molecule	getScaffoldOrientatedHit(Molecule scaffold, Molecule molToAlign) Only for internal use!
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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:

scaffold - baseline for alignment

molToAlign - molecule that should be aligned to scaffold

hit - ordered array (its size must be equal scaffold size), describes matchings between scaffold and molToAlign atom indices (e.g. scaffold[2] --> molToAlign[5] ==> hit[2] = 5)

Returns:

aligned molecule

color

public static void color(Molecule substructure,
                         Molecule molToColor,
                         HitColoringAndAlignmentOptions options)

Performs hit coloring on the specified structure

Parameters:

substructure - the structure taken as a template for coloring

molToColor - the structure to be colored

hit - maps toms fo the template to atoms in the colored structure

options - coloring options

color

public static void color(Molecule substructure,
                         Molecule molToColor,
                         int[] hit,
                         HitColoringAndAlignmentOptions options)

Performs hit coloring on the specified structure

Parameters:

substructure - the structure taken as a template for coloring

molToColor - the structure to be colored

hit - maps toms fo the template to atoms in the colored structure

options - coloring options

getNonHitBonds

protected static java.util.ArrayList getNonHitBonds(Molecule query,
                                                    Molecule target,
                                                    int[] hit)

Returns the bonds of the target molecule that should not be colored in hit highlighting. Bonds surrounding lonely atoms are never included

Parameters:

query - the query Molecule

target - the target Molecule

hit - the hit list

Returns:

the non-hit bonds specified by the atom indexes of their endpoints. The ArrayList contains MolBond objects.

Since:

JChem 2.2