chemaxon.util
Class HitDisplayTool

java.lang.Object
  chemaxon.util.HitDisplayTool

All Implemented Interfaces:

chemaxon.license.Licensable, SearchConstants

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 hco = new HitColoringAndAlignmentOptions();
  hco.coloring = true;
  hco.alignmentMode = align;
  hco.markushDisplayMode = //set the desired markush display mode
  MolSearchOptions mso = ... //get you search options
  Molecule query = ... //get your query
  HitDisplayTool hdt = new HitDisplayTool(hco, mso, null, query);
  
  //retrieve all hits:
  Molecule[] hits = hdt.getHits(m, (Molecule) null, 0);
  
  //or retrieve the hits one-by-one:
  HitDisplayTool hdt2 = new HitDisplayTool(hco, mso, null, query);
  hdt2.setTarget(m);
  ArrayList hitList = new ArrayList();
  Molecule hit = hdt2.getNextHit();
  while(hit!=null) {
        hitList.add(hit);
        hit = hdt2.getNextHit();
  }
  
  

Since:

JChem 5.0

Author:

Szilard Dorant, Vencel Bors Date: Nov 04, 2010

See Also:

VisualizationExample.java

Field Summary

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, 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_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MARKUSH_MCS, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, 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, 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

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

Method Summary

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, byte[] markushSource, int maxHitCount) 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	setMoleculeMarkushSourceTarget(Molecule targetMol, byte[] markushSource) 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,
                      Standardizer standardizer,
                      Molecule query)

Constructor.

Parameters:

options - options for coloring and alignment

searchOptions - search options

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

query - the query structure

Method Detail

getHit

public Molecule getHit(Molecule targetMol)
                throws chemaxon.sss.search.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:

chemaxon.sss.search.SearchException - error during searching

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

getHits

public Molecule[] getHits(Molecule targetMol,
                          byte[] markushSource,
                          int maxHitCount)
                   throws MolFormatException,
                          chemaxon.enumeration.supergraph.SupergraphException,
                          chemaxon.sss.search.SearchException

Processes the next target structure.

Parameters:

targetMol - the target

markushSource - a markush structure can be specified here, or null. The proper byte[] can be obtained from the database cd_markush field.

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:

MolFormatException

chemaxon.enumeration.supergraph.SupergraphException

chemaxon.sss.search.SearchException

getHits

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

chemaxon.sss.search.SearchException

setTarget

public void setTarget(Molecule targetMol)

Sets the target structure.

Parameters:

targetMol - the target

setMoleculeMarkushSourceTarget

public void setMoleculeMarkushSourceTarget(Molecule targetMol,
                                           byte[] markushSource)
                                    throws MolFormatException,
                                           java.util.ServiceConfigurationError

Sets the target structure.

Parameters:

targetMol - the target

markushSource - a markush structure can be specified here, or null. The proper byte[] can be obtained from the database cd_markush field.

Throws:

MolFormatException - markushSource is not of a suitable format

Ille - the markush structure read from the byte array has bad structure.

java.util.ServiceConfigurationError

getHits

public Molecule[] getHits(int maxHitCountIn)
                   throws chemaxon.sss.search.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.sss.search.SearchException

chemaxon.enumeration.supergraph.SupergraphException

See Also:

setTarget(Molecule), setMoleculeMarkushSourceTarget(Molecule, byte[])

getNextHit

public Molecule getNextHit()
                    throws chemaxon.sss.search.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.sss.search.SearchException

chemaxon.enumeration.supergraph.SupergraphException

See Also:

setTarget(Molecule), setMoleculeMarkushSourceTarget(Molecule, byte[])

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