chemaxon.util

Class HitDisplayTool

java.lang.Object

chemaxon.util.HitDisplayTool

All Implemented Interfaces:

chemaxon.license.Licensable, SearchConstants

@PublicAPI
public class HitDisplayTool
extends java.lang.Object
implements SearchConstants, chemaxon.license.Licensable

Class for displaying hit results with hit coloring, alignment, partial clean, etc. E.g.

  HitColoringAndAlignmentOptions displayOpts = new HitColoringAndAlignmentOptions();
  displayOpts.setColoringEnabled(true);
  displayOpts.setAlignmentMode(align);
  // ...
  MolSearchOptions searchOpts = ... // set search options
  Molecule query = ... // set your query
  HitDisplayTool hdt = new HitDisplayTool(displayOpts, searchOpts, query);
  
  // Retrieve all hits
  Molecule[] hits = hdt.getHits(m, (Molecule) null, 0);
  
  // Or retrieve the hits one-by-one
  HitDisplayTool hdt2 = new HitDisplayTool(displayOpts, searchOpts, query);
  hdt2.setTarget(m);
  List<Molecule> hitList = new ArrayList<Molecule>();
  Molecule hit = hdt2.getNextHit();
  while (hit != null) {
        hitList.add(hit);
        hit = hdt2.getNextHit();
  }
 

Since:

JChem 5.0

Author:

Szilard Dorant, Vencel Bors

Field Summary

Fields

Modifier and Type	Field and Description
static int	HIT_ATOM_SET Set identifier for hit atoms
static int	HIT_BOND_SET Set identifier for hit bonds
static int	NON_HIT_ATOM_SET Set identifier for non-hit atoms
static int	NON_HIT_BOND_SET Set identifier for non hit bonds

Fields inherited from interface chemaxon.sss.SearchConstants

ABS_STEREO_ALWAYS_ON, ABS_STEREO_CHIRAL_FLAG, ABS_STEREO_TABLE_OPTION, ATTACHED_DATA_MATCH_EXACT, ATTACHED_DATA_MATCH_GENERAL, ATTACHED_DATA_MATCH_IGNORE, ATTACHMENT_ATOM, ATTACHMENT_LABEL, ATTACHMENT_MAP, ATTACHMENT_NONE, ATTACHMENT_POINT, ATTACHMENT_RLABEL, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SEARCHTYPE, DISSIMILARITY_PROPERTY_NAME, DUPLICATE, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_ORDERING_NONE, HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, IMPLICIT_H_MATCHING_IGNORE, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, POSITION_ON_0TH_HEAVY_ATOM, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_TYPE_NAMES, SIMILARITY, STEREO_DIASTEREOMER, STEREO_ENANTIOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_DEFAULT, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_GROUP_H, UNDEF_R_MATCHING_GROUP_H_EMPTY, UNDEF_R_MATCHING_UNDEF_R, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL_HALF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF

Constructor Summary

Constructors

Constructor and Description
HitDisplayTool(HitColoringAndAlignmentOptions options, MolSearchOptions searchOptions, Molecule query) Creates a new instance with the specified parameters, with using a default standardization method which applies only aromatization during the search process.
HitDisplayTool(HitColoringAndAlignmentOptions options, MolSearchOptions searchOptions, Molecule query, Standardizer standardizer) Constructor.
HitDisplayTool(HitColoringAndAlignmentOptions hco, chemaxon.sss.search.pipeline.SearchSettings settings, Molecule query, Standardizer standardizer) Constructor.

Method Summary

Modifier and Type	Method and Description
Molecule	getHit(Molecule targetMol) Processes the next target structure.
java.util.ArrayList<int[]>	getHitIndexes() Returns the hit indexes for the last target.
Molecule[]	getHits(int maxHitCountIn) Processes the next target structure.
Molecule[]	getHits(Molecule targetMol, Molecule markush, int maxHitCount) Processes the next target structure.
Molecule	getNextHit() Gets the next hit.
boolean	isLicensed()
void	setLicenseEnvironment(java.lang.String env)
void	setMoleculeAndMarkushTarget(Molecule targetMol, Molecule markushInnerRepresentation) Sets the target structure.
void	setTarget(Molecule targetMol) Sets the target structure.

Methods inherited from class java.lang.Object

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

Field Detail

HIT_ATOM_SET

public static final int HIT_ATOM_SET

Set identifier for hit atoms

See Also:

Constant Field Values

NON_HIT_ATOM_SET

public static final int NON_HIT_ATOM_SET

Set identifier for non-hit atoms

See Also:

Constant Field Values

HIT_BOND_SET

public static final int HIT_BOND_SET

Set identifier for hit bonds

See Also:

Constant Field Values

NON_HIT_BOND_SET

public static final int NON_HIT_BOND_SET

Set identifier for non hit bonds

See Also:

Constant Field Values

Constructor Detail

HitDisplayTool

public HitDisplayTool(HitColoringAndAlignmentOptions options,
                      MolSearchOptions searchOptions,
                      Molecule query,
                      Standardizer standardizer)

Constructor.

Parameters:

options - options for coloring and alignment

searchOptions - search options

query - the query structure

standardizer - the Standardizer which will be used during the search process, or null for only aromatization.

HitDisplayTool

public HitDisplayTool(HitColoringAndAlignmentOptions options,
                      MolSearchOptions searchOptions,
                      Molecule query)

Creates a new instance with the specified parameters, with using a default standardization method which applies only aromatization during the search process.

Parameters:

options - options for coloring and alignment

searchOptions - search options

query - the query structure

HitDisplayTool

@Beta
public HitDisplayTool(HitColoringAndAlignmentOptions hco,
                            chemaxon.sss.search.pipeline.SearchSettings settings,
                            Molecule query,
                            Standardizer standardizer)

Constructor. For internal use only!

Parameters:

hco - options for coloring and alignment

settings - search settings containing search options among others

query - the query structure

standardizer - the Standardizer which will be used during the search process, or null for only aromatization.

Method Detail

getHit

public Molecule getHit(Molecule targetMol)
                throws SearchException,
                       chemaxon.enumeration.supergraph.SupergraphException

Processes the next target structure.

Parameters:

targetMol - the target

Returns:

the structure to be displayed, or null if there was no hit

Throws:

SearchException - error during searching

chemaxon.enumeration.supergraph.SupergraphException - if target is a markush structure but is erroneous

getHits

public Molecule[] getHits(Molecule targetMol,
                          Molecule markush,
                          int maxHitCount)
                   throws chemaxon.enumeration.supergraph.SupergraphException,
                          SearchException

Processes the next target structure.

Parameters:

targetMol - the target

markush - a markush structure can be specified here, or null

maxHitCount - specify 0 to get back all the hits found, or an arbitrary limit.
Specify -1 to get back only a single hit, the best fitting is returned in case of alignment (default).

Returns:

the structures to be displayed, or a zero sized array if there were no hits

Throws:

chemaxon.enumeration.supergraph.SupergraphException - in case of search failure

SearchException - in case of search failure

setTarget

public void setTarget(Molecule targetMol)

Sets the target structure.

Parameters:

targetMol - the target

setMoleculeAndMarkushTarget

@Beta
public void setMoleculeAndMarkushTarget(Molecule targetMol,
                                              Molecule markushInnerRepresentation)
                                       throws chemaxon.enumeration.supergraph.SupergraphException

Sets the target structure.

Parameters:

targetMol - the target

markushInnerRepresentation - if the target molecule is a markush molecule and its inner representation is known it can be specified here, otherwise this parameter should be set to null.

Throws:

chemaxon.enumeration.supergraph.SupergraphException - in case of search failure

getHits

public Molecule[] getHits(int maxHitCountIn)
                   throws SearchException,
                          chemaxon.enumeration.supergraph.SupergraphException

Processes the next target structure. Before calling this function the target has to be set.

Parameters:

maxHitCountIn - specify 0 to get back all the hits found, or an arbitrary limit.
Specify -1 to get back only a single hit, the best fitting is returned in case of alignment (default).

Returns:

the structures to be displayed, or a zero sized array if there were no hits

Throws:

chemaxon.enumeration.supergraph.SupergraphException - in case of search failure

SearchException - in case of search failure

See Also:

setTarget(Molecule), setMoleculeAndMarkushTarget(Molecule, Molecule)

getNextHit

public Molecule getNextHit()
                    throws SearchException,
                           chemaxon.enumeration.supergraph.SupergraphException

Gets the next hit. Before calling this method the target has to be set.

Returns:

the next colored hit or null if no more hits are present

Throws:

chemaxon.enumeration.supergraph.SupergraphException - in case of search failure

SearchException - in case of search failure

See Also:

setTarget(Molecule), setMoleculeAndMarkushTarget(Molecule, Molecule)

getHitIndexes

public java.util.ArrayList<int[]> getHitIndexes()

Returns the hit indexes for the last target. Can be called after getHit(Molecule), getHits(int) or getNextHit()

Returns:

the hit indexes in an ArrayList, containing int[] elements.

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable