chemaxon.util

Class HitDisplayUtil

java.lang.Object

chemaxon.util.HitDisplayUtil

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

Author:

Szilard Dorant, Tamas Csizmazia

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROP_ALIGNHIT Atom property to store "align hit" option.

Constructor Summary

Constructors

Constructor and Description
HitDisplayUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static void	color(Molecule substructure, Molecule molToColor, HitColoringAndAlignmentOptions options) Only for internal use!
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.
protected static ArrayList<MolBond>	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.
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.

Methods inherited from class java.lang.Object

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

Field Detail

PROP_ALIGNHIT

public static final String PROP_ALIGNHIT

Atom property to store "align hit" option.

See Also:

Constant Field Values

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)

Only for internal use!

Parameters:

substructure - the structure taken as a template for coloring

molToColor - the structure to be colored

options - coloring options

getNonHitBonds

protected static ArrayList<MolBond> 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 Bonds between targets atoms belonging to the same query atom are also accepted. e.g. qHomology see setMultiAtomHitColor(Molecule, Molecule, int[]).

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