chemaxon.sss.search
Class RGroupDecomposition

java.lang.Object
  chemaxon.sss.search.Search
      chemaxon.sss.search.MolSearch
          chemaxon.sss.search.StandardizedMolSearch
              chemaxon.sss.search.RGroupDecomposition

All Implemented Interfaces:

chemaxon.license.Licensable, SearchConstants, StereoConstants, chemaxon.util.search.MolSearcher

public class RGroupDecomposition
extends StandardizedMolSearch
implements chemaxon.license.Licensable

R-group decomposition.

Given a scaffold structure with attached R1, R2, ... nodes as query, determines the possible R-group decompositions of given target molecule. A decomposition consists of the matching scaffold and the R1, R2, ... ligands with attachment points. Each decomposition corresponds to a group hit, see Search.findFirstGroup() and Search.findNextGroup().

After setting the query, the target, and possibly the search options, call findFirstDecomposition() and findNextDecomposition() to get the decompositions. Call Decomposition.equals(java.lang.Object) to filter equivalent decompositions that provide the same ligands (but correspond to different group hits). Color the decomposition by calling Decomposition.color() or Decomposition.color(java.lang.String). To create a result table with all decompositions right away, call findLigandTable(int, int, java.lang.String). Alternatively, you can get the table header with query, target and R-atoms, call getLigandTableHeader(int, int, java.lang.String) and then add only a single table row corresponding to the first decomposition by calling findLigandTableRow(int, java.lang.String). Different ligand attachment types can be set in setAttachmentType(int). As of JChem 5.3, extra ligands without matching R-atom are not allowed. As of JChem 5.3, a query without R-atoms will be automatically modified in setQuery(chemaxon.struc.Molecule): R-atoms will be added in place of implicit hydrogens by addRGroups(chemaxon.struc.Molecule). The R-grouped query can be retrieved by getRGroupedQuery(). If the original query contains R-atoms then the default R-atom matching behavior is SearchConstants.UNDEF_R_MATCHING_GROUP_H, otherwise the default matching behavior of the automatically added R-atoms is SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY (the empty set matching is allowed here because we expect that ligands are attached to some of the implicit hydrogens in the original query, but not necessarily all implicit hydrogens have corresponding ligands).

Search options:

The options below have different default values as in MolSearch:

• SearchOptions.setRLigandEqualityCheck(boolean): sets whether undefined R-atoms with the same R-group ID should match the same structure. Default: true.
• SearchOptions.setBridgingRAllowed(boolean value): sets whether different undefined R-atoms can match the same group of atoms. Default: true.
• SearchOptions.setUndefinedRAtom(int): sets the matching behavior of an undefined R atom in the query. Default: SearchConstants.UNDEF_R_MATCHING_GROUP_H if the original query has R-atoms, SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY with automatically added R-atoms in place of implicit hydrogens otherwise. Note, that unlike other search options, this option should be specified together with the query in setQuery(chemaxon.struc.Molecule, int).

API usage examples:

query: the query molecule
target: the target molecule

• Set parameters, get decomposition results, color target according to decomposition in SDF tag:

   RGroupDecomposition rgd = new RGroupDecomposition();
  
   // set search options
   rgd.getSearchOptions().setRLigandEqualityCheck(false);
   rgd.getSearchOptions().setBridgingRAllowed(false);
  
   // set query and target with specific R-atom matching
   rgd.setQuery(query, SearchOptions.UNDEF_R_MATCHING_GROUP);
   rgd.setTarget(target);
  
   // find decompositions, output colored and aligned target
   MolExporter exporter = new MolExporter(System.out, "sdf:-a");  
   ArrayList list = new ArrayList ();
   Decomposition d = rgd.findFirstDecomposition();
   while (d != null) {
       boolean duplicate = false;
       for (int i=list.size()-1; i >= 0; --i) {
             if (d.equals(list.get(i))) {
               duplicate = true;
               break;
           }
       }
       if (!duplicate) {
             list.add(d);
           d.color("DMAP");
           exporter.write(d.getTarget());
       }
       d = rgd.findNextDecomposition();
   }      
   exporter.close();
   

• Get non-scaffold ligands, standardize both query and targets, output ligands in first decomposition:

   // standardize query and targets to find hits
   // in most cases aromatization only will be sufficient
   Standardizer st = new Standardizer("aromatize..N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]");
  
   RGroupDecomposition rgd = new RGroupDecomposition();
   rgd.setAttachmentType(RGroupDecomposition.ATTACHMENT_MAP);
  
   // standardize and set query
   st.standardize(query);
   rgd.setQuery(query);
  
   // standardize and set target
   st.standardize(target);
   rgd.setTarget(target);
      
   // process decomposition, output ligands
   Decomposition d = rgd.findDecomposition();
   if (d != null) {
       Molecule[] ligands = d.getLigands();
       for (Molecule ligand : ligands) {
           if (ligand != null) {
               System.out.println(ligand.toFormat("smiles"));
           }
       }
   }
   

• Color decomposition in atom sets, align target and ligands according to query, output in MRV:

   RGroupDecomposition rgd = new RGroupDecomposition();
   rgd.setAttachmentType(RGroupDecomposition.ATTACHMENT_POINT); 
   rgd.setAlign(true);
   rgd.setQuery(query);
   rgd.setTarget(target);
   MolExporter exporter = new MolExporter(System.out, "mrv:-a");
  
   Decomposition d = rgd.findDecomposition();
   if (d != null) {
       d.color();
       Molecule[] ligands = d.getLigands();
       Molecule scaffold = d.getScaffold();
       for (Molecule ligand : ligands) {
             if (ligand != null) {
                 exporter.write(ligand);
             } else {
               exporter.write(scaffold); 
           }
       }
   }
  
   exporter.close();
   

• Image export with target coloring:

   // standardize query and targets to find hits
   // in most cases aromatization only will be sufficient
   Standardizer st = new Standardizer("aromatize..N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]");
  
   // init RGroupDecomposition
   RGroupDecomposition rgd = new RGroupDecomposition();
  
   // set target and ligand alignment according to query
   rgd.setAlign(true);
  
   // set attachment data in atom labels as "R1", "R2", ...
   rgd.setAttachmentType(RGroupDecomposition.ATTACHMENT_RLABEL);
  
   // standardize and set query
   st.standardize(query);
   rgd.setQuery(query);
  
   // standardize and set target
   st.standardize(target);
   rgd.setTarget(target);
      
   // process decompositions
   int index = 0;
   Decomposition d = null;
   if ((d = rgd.findDecomposition()) != null) {
       ++index;
  
       // color in atom sets
       d.color();
  
       // get the colored target
       Molecule mol = d.getTarget();
  
       // convert to PNG with default set colors 
       // 'mono' option is needed to supress the default CPK atom coloring
       byte[] png = mol.toBinFormat("png:-a,mono,setcolors");
  
       // write to file
       BufferedOutputStream os = new BufferedOutputStream(new FileOutputStream("img-"+index+".png"));
       os.write(png, 0, png.length);
       os.flush();
       os.close();
  
       // get the query from the decomposition (possibly with automatically added R-atoms):
       Molecule rgquery = d.getQuery();
  
       // get the colored ligands
       Molecule[] ligands = d.getLigands();
       for (int i=0; i < ligands.length; ++i) {
             if (ligands[i] != null) {
                 png = ligands[i].toBinFormat("png:-a,mono,setcolors");
                 os = new BufferedOutputStream(
                        new FileOutputStream("img-"+index+"-R"+rgquery.getAtom(i).getRgroup()+".png"));
                 os.write(png, 0, png.length);
                 os.flush();
                 os.close();      
             }
       }          
   }
   

• Get a colored ligand table with coloring data set in the "DMAP" SDF tag:

   RGroupDecomposition rgd = new RGroupDecomposition();
   rgd.setAttachmentType(RGroupDecomposition.ATTACHMENT_ATOM); // attachment type: any-atoms
   rgd.setQuery(query);
   rgd.setTarget(target);
   Molecule[][] ligandTable = rgd.findLigandTable(RGroupDecomposition.HEADER_RGROUP,
       RGroupDecomposition.COL_MOLECULE | RGroupDecomposition.COL_SCAFFOLD, "DMAP");
   

• Get a colored ligand table for different targets, one row for each target corresponding to the first decomposition (note, that this is null if there is no hit), align target and ligands according to query, coloring data set in atom sets (for MRV output):

   RGroupDecomposition rgd = new RGroupDecomposition();
   rgd.setAttachmentType(RGroupDecomposition.ATTACHMENT_MAP);
   rgd.setAlign(true);
   rgd.setQuery(query);
   Molecule[][] ligandTable = new Molecule[targets.length+1][];
   ligandTable[0] = rgd.getLigandTableHeader(RGroupDecomposition.HEADER_MAP, 
       RGroupDecomposition.COL_MOLECULE);
   for (int i=0; i < targets.length; ++i) {
       rgd.setTarget(targets[i]);
       ligandTable[i+1] = rgd.findLigandTableRow(RGroupDecomposition.COL_MOLECULE);
   }
   

• Get ligands corresponding to R1 atoms:

   // standardize query and targets to find hits
   // in most cases this is not needed, since the 
   // default standardization (aromatization only) will be sufficient
   Standardizer st = new Standardizer("aromatize..N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]");
  
   // init RGroupDecomposition, set query
   RGroupDecomposition rgd = new RGroupDecomposition();
   rgd.setAttachmentType(RGroupDecomposition.ATTACHMENT_MAP);
   rgd.getSearchOptions().setRLigandEqualityCheck(false);
  
   // standardize and set query
   st.standardize(query);
   rgd.setQuery(query);
  
   // standardize and set target
   st.standardize(target);
   rgd.setTarget(target);
  
   // process decomposition
   Decomposition d = rgd.findDecomposition();
   if (d != null) {
  
       // get query from decomposition, possibly R-atoms added automatically:
       Molecule rgquery = d.getQuery();
  
       // get the ligands:
       Molecule[] ligands = d.getLigands();
  
       // look for R1 ligands:
       for (int i=0; i < ligands.length; ++i) {
           if ((rgquery.getAtom(i).getAtno() == MolAtom.RGROUP) && 
               (rgquery.getAtom(i).getRgroup() == 1)) {
               if (ligands[i] != null) {
                   System.out.println(ligands[i].toFormat("smiles"));
               }
           }
       }
   }
   

Since:

JChem 3.0

Author:

Nora Mate

Field Summary

static int	ATTACHMENT_ATOM Constant for attachment point representation in ligands: sets attachment points by attaching an pseudo-atom.
static int	ATTACHMENT_LABEL Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...
static int	ATTACHMENT_MAP Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int).
static int	ATTACHMENT_NONE Constant for attachment point representation in ligands: none (no attachment point data).
static int	ATTACHMENT_POINT Constant for attachment point representation in ligands: sets attachment points by MolAtom.addRgroupAttachmentPoint(int, int).
static int	ATTACHMENT_RLABEL Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String).
static int	COL_MOLECULE Constant for adding query-target column to ligand table.
static int	COL_SCAFFOLD Constant for adding scaffold column to ligand table.
static int	HEADER_MAP Constant for header type: header with any atoms mapped by Rgroup indexes.
static int	HEADER_NONE Constant for header type: no header.
static int	HEADER_RGROUP Constant for header type: header with Rgroup atoms (cannot be exported to SMILES).
static java.lang.String	SEPARATOR Separator in atom color code property string representation.

Fields inherited from class chemaxon.sss.search.MolSearch

isOrigTargetMayBeMarkush, isQueryStandardizable, isTargetStandardizable

Fields inherited from class chemaxon.sss.search.Search

MRV_OUTPUT_LEVEL, preMatchLength, preMatchQueryAtoms, preMatchTargetAtoms, searchOptions

Fields inherited from interface chemaxon.struc.StereoConstants

ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

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

RGroupDecomposition()
Constructor.

Method Summary

static void	addHydrogens(Molecule query) Deprecated. as of JChem 5.3, full fragment matching is forced, which means that ligands are accepted at R-atoms only (and never in place of implicit hydrogens)
static void	addRGroups(Molecule query) Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s.
static void	addRGroups(Molecule query, int bondType) Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s.
Decomposition	findDecomposition() Finds the first decomposition result.
Decomposition	findDecomposition(boolean first) Finds a decomposition result.
Decomposition	findFirstDecomposition() Finds the first decomposition result.
Molecule[][]	findLigandTable(int headerType, int addCols) Returns the ligand table.
Molecule[][]	findLigandTable(int headerType, int addCols, java.lang.String colorTag) Returns the ligand table.
Molecule[]	findLigandTableRow(int addCols) Returns a ligand table row with ligands corresponding to a the first search hit.
Molecule[]	findLigandTableRow(int addCols, java.lang.String colorTag) Returns a ligand table row with ligands corresponding to a the first search hit.
Decomposition	findNextDecomposition() Finds the next decomposition result.
Molecule[]	getLigandTableHeader(int headerType, int addCols) Returns ligand table header.
Molecule[]	getLigandTableHeader(int headerType, int addCols, java.lang.String colorTag) Returns ligand table header.
Molecule	getQuery() Retrieves the original query structure.
Molecule	getRGroupedQuery() Returns the R-grouped query.
boolean	isLicensed() Gets whether searching is included in the user licence.
boolean	isMarkushQuery() Returns true if query contains Markush features which will be enumerated (all features except defined R-rgroups and homologies).
void	setAlign(boolean align) Sets alignment.
void	setAttachmentType(int type) Sets the attachment point representation type in ligand molecules.
void	setLicenseEnvironment(java.lang.String env) Set the license to be used by the search object.
void	setQuery(Molecule mol) Specifies the query structure to search for.
void	setQuery(Molecule mol, int undefinedRAtom) Specifies the query structure to search for.
void	setSameRGroupSameStructure(boolean sameRGroupSameStructure) Deprecated. as of JChem 5.3, set search option "RLigandEqualityCheck" in SearchOptions, see SearchOptions.setRLigandEqualityCheck(boolean) and SearchOptions.setOption(java.lang.String, java.lang.String)
void	setTarget(Molecule mol) Specifies the target molecule to search in.

Methods inherited from class chemaxon.sss.search.StandardizedMolSearch

setStandardizer

Methods inherited from class chemaxon.sss.search.MolSearch

addComparator, addMatch, addMatch, checkFilter, checkFilter, clearComparators, clearMatch, filter, findAllHits, findFirstHit, findNextHit, getFilter, getMatchingQuery, getMatchingTarget, getTarget, hasFilter, hasHitFilter, isMatching, removeComparator, setFilter, setFilterConfig, setOrigTargetMayBeMarkush, setQuery, setQuery, setSearchOptions, setTarget, stop

Methods inherited from class chemaxon.sss.search.Search

areMatchingBondTypes, areMatchingBondTypes, findAll, findAllGroups, findFirst, findFirstGroup, findNext, findNextGroup, getAtomStereo, getMatchCount, getQueryAsString, getQueryToPrint, getSearchOptions, getTargetAsString, getTargetToPrint, isMatchCountBetween, isMatchCountInRelation, isVerbose, logException, setSearchOptions, setVerbose

Methods inherited from class java.lang.Object

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

Field Detail

COL_MOLECULE

public static final int COL_MOLECULE

Constant for adding query-target column to ligand table.

See Also:

Constant Field Values

COL_SCAFFOLD

public static final int COL_SCAFFOLD

Constant for adding scaffold column to ligand table.

See Also:

Constant Field Values

HEADER_NONE

public static final int HEADER_NONE

Constant for header type: no header.

See Also:

Constant Field Values

HEADER_RGROUP

public static final int HEADER_RGROUP

Constant for header type: header with Rgroup atoms (cannot be exported to SMILES).

See Also:

Constant Field Values

HEADER_MAP

public static final int HEADER_MAP

Constant for header type: header with any atoms mapped by Rgroup indexes.

See Also:

Constant Field Values

SEPARATOR

public static final java.lang.String SEPARATOR

Separator in atom color code property string representation.

See Also:

Constant Field Values

ATTACHMENT_NONE

public static final int ATTACHMENT_NONE

Constant for attachment point representation in ligands: none (no attachment point data).

See Also:

Constant Field Values

ATTACHMENT_POINT

public static final int ATTACHMENT_POINT

Constant for attachment point representation in ligands: sets attachment points by MolAtom.addRgroupAttachmentPoint(int, int). This is the default.

See Also:

Constant Field Values

ATTACHMENT_MAP

public static final int ATTACHMENT_MAP

Constant for attachment point representation in ligands: sets attachment points by MolAtom.setAtomMap(int). Maps with R-group ID: 1 for R1, 2 for R2, ...

See Also:

Constant Field Values

ATTACHMENT_LABEL

public static final int ATTACHMENT_LABEL

Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String) Labels with R-group ID: "1" for R1, "2" for R2, ...

See Also:

Constant Field Values

ATTACHMENT_RLABEL

public static final int ATTACHMENT_RLABEL

Constant for attachment point representation in ligands: sets attachment points by MolAtom.setExtraLabel(java.lang.String). Labels with full R-atom name: "R1" for R1, "R2" for R2, ...

See Also:

Constant Field Values

ATTACHMENT_ATOM

public static final int ATTACHMENT_ATOM

Constant for attachment point representation in ligands: sets attachment points by attaching an pseudo-atom.

See Also:

Constant Field Values

Constructor Detail

RGroupDecomposition

public RGroupDecomposition()

Constructor.

Method Detail

setAttachmentType

public void setAttachmentType(int type)

Sets the attachment point representation type in ligand molecules. Possible values:

• ATTACHMENT_NONE
• ATTACHMENT_POINT (default)
• ATTACHMENT_MAP
• ATTACHMENT_LABEL
• ATTACHMENT_RLABEL
• ATTACHMENT_ATOM

Parameters:

type - is the attachment point representation type

setSameRGroupSameStructure

public void setSameRGroupSameStructure(boolean sameRGroupSameStructure)

Deprecated. as of JChem 5.3, set search option "RLigandEqualityCheck" in SearchOptions, see SearchOptions.setRLigandEqualityCheck(boolean) and SearchOptions.setOption(java.lang.String, java.lang.String)

Sets the "same R-group symbol matches same ligands" property. If set to true then identical R-group symbols on the query (e.g. two R1-s) should match identical target ligands. If set to false then identical R-group symbols on the query only represent equivalent positions but may match different structures. Default: true.

Parameters:

sameRGroupSameStructure - is true identical R-group symbols on the query should match identical target ligands

Since:

JChem 3.1

addHydrogens

public static void addHydrogens(Molecule query)

Deprecated. as of JChem 5.3, full fragment matching is forced, which means that ligands are accepted at R-atoms only (and never in place of implicit hydrogens)

Adds explicit hydrogens to query molecule to force ligands to be attached at Rgroup atoms only (full fragment matching). Call this before setQuery(Molecule).

Parameters:

query - is the query molecule to be set

See Also:

addRGroups(Molecule)

addRGroups

public static void addRGroups(Molecule query)

Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s. In this way ligands will be accepted and stored at all possible attachments. As of JChem 5.3, these R-atoms are added automatically if the query does not contain undefined R-atoms. In this case R-atoms are allowed to match the empty set. Call this before setQuery(Molecule).

Parameters:

query - is the query molecule to be set

See Also:

addHydrogens(Molecule)

addRGroups

public static void addRGroups(Molecule query,
                              int bondType)

Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s. Bond types: see constants in MolBond. In this way ligands will be accepted and stored at all possible attachments. Call this before setQuery(Molecule).

Parameters:

query - is the query molecule to be set

bondType - is the attachment bond type

See Also:

addHydrogens(Molecule)

setAlign

public void setAlign(boolean align)

Sets alignment. Default: false.

Parameters:

align - is true if ligands and target should be aligned (cleaned)

Since:

JChem 5.3

isMarkushQuery

public boolean isMarkushQuery()

Returns true if query contains Markush features which will be enumerated (all features except defined R-rgroups and homologies).

Returns:

true if query contains Markush features other than defined R-groups and homologies

setQuery

public void setQuery(Molecule mol,
                     int undefinedRAtom)

Specifies the query structure to search for. If the query does not contain undefined R-atoms then addRGroups(chemaxon.struc.Molecule) is called to put R-atoms in place of implicit hydrogens.

Parameters:

mol - the standardized query structure.

undefinedRAtom - the undefined R-atom setting, possible values:

• SearchConstants.UNDEF_R_MATCHING_GROUP: R-atom matches heavy atom group
• SearchConstants.UNDEF_R_MATCHING_GROUP_H: R-atom matches heavy atom group or hydrogen
• SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY: R-atom matches heavy atom group, hydrogen or the empty set

See note on aromatic bonds.

Since:

JChem 5.3

setQuery

public void setQuery(Molecule mol)

Specifies the query structure to search for. If the query does not contain undefined R-atoms then addRGroups(chemaxon.struc.Molecule) is called to put R-atoms in place of implicit hydrogens - in this case undefined R-atoms are allowed to match the empty set, apart from heavy atom groups or hydrogen atoms. If the query contains R-atoms, these are allowed to match heavy atom groups or hydrogen atoms, but not the empty set. The R-atom matching behavior can be explicitly set in setQuery(chemaxon.struc.Molecule, int).

Specified by:

setQuery in interface chemaxon.util.search.MolSearcher

Overrides:

setQuery in class MolSearch

Parameters:

mol - the standardized query structure. See note on aromatic bonds.

See Also:

setQuery(chemaxon.struc.Molecule, int)

setTarget

public void setTarget(Molecule mol)

Specifies the target molecule to search in.

Specified by:

setTarget in interface chemaxon.util.search.MolSearcher

Overrides:

setTarget in class MolSearch

Parameters:

mol - the possibly standardized target molecule. See note on aromatic bonds.

getQuery

public Molecule getQuery()

Retrieves the original query structure.

Overrides:

getQuery in class MolSearch

Returns:

the original query structure

getRGroupedQuery

public Molecule getRGroupedQuery()

Returns the R-grouped query. This is the original query if it contains undefined R-atoms, otherwise it is its R-rgouped version. This is the query structure used in the search process.

Returns:

the R-grouped query

Since:

JChem 5.3

findFirstDecomposition

public Decomposition findFirstDecomposition()
                                     throws chemaxon.sss.search.SearchException

Finds the first decomposition result.

Returns:

the decomposition corresponding to the first group hit, or null if there is no hit

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

See Also:

findNextDecomposition(), findDecomposition(), findDecomposition(boolean)

findNextDecomposition

public Decomposition findNextDecomposition()
                                    throws chemaxon.sss.search.SearchException

Finds the next decomposition result.

Returns:

the decomposition corresponding to the next group hit, or null if there is no hit

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

See Also:

findFirstDecomposition(), findDecomposition(), findDecomposition(boolean)

findDecomposition

public Decomposition findDecomposition()
                                throws chemaxon.sss.search.SearchException

Finds the first decomposition result. Just a shorthand for findFirstDecomposition().

Returns:

the decomposition corresponding to the first group hit, or null if there is no hit

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

See Also:

findFirstDecomposition(), findNextDecomposition(), findDecomposition(boolean)

findDecomposition

public Decomposition findDecomposition(boolean first)
                                throws chemaxon.sss.search.SearchException

Finds a decomposition result.

Parameters:

first - true if first decomposition, false if next decomposition

Returns:

the decomposition corresponding to the first/next group hit, or null if there is no hit

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

See Also:

findFirstDecomposition(), findNextDecomposition(), findDecomposition()

findLigandTable

public Molecule[][] findLigandTable(int headerType,
                                    int addCols)
                             throws chemaxon.sss.search.SearchException

Returns the ligand table. Format:

 query    scaffold        R1         R2         R3    ...
 ---------------------------------------------------------
 target   scaffold1    ligand1.1  ligand1.2  ligand1.3
 target   scaffold2    ligand2.1  ligand2.2  ligand2.3
 

in a Molecule[][] array (table):

• table[0]: the table header with Rgroups as 1-atom molecules
• table[i], i > 0: target molecule, scaffold, ligands

If there are more Rgroup ligands with the same rgroup index in the query (e.g. multiple R1 groups) then corresponding ligands will be fused. If there is no Rgroup ligand with an rgroup index then the corresponding table entry is null. Color map is stored in atom sets which can be written in MRV format and is automatically handled by MView. See MolAtom.getSetSeq(). Rgroups in the table header are represented by any-atoms with rgroup index set in atom map to enable SMILES export.

Parameters:

headerType - is the header type:

• HEADER_NONE for no header
• HEADER_RGROUP for header with rgroup atoms (cannot be exported to SMILES)
• HEADER_MAP for mapped any atoms (for SMILES export)

addCols - additional columns to include:

• COL_MOLECULE for including the target,
• COL_SCAFFOLD for including the scaffold,
• COL_MOLECULE | COL_SCAFFOLD for both,
• 0 for none

Returns:

the molecule table

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

findLigandTable

public Molecule[][] findLigandTable(int headerType,
                                    int addCols,
                                    java.lang.String colorTag)
                             throws chemaxon.sss.search.SearchException

Returns the ligand table. Format:

 query    scaffold        R1         R2         R3    ...
 ---------------------------------------------------------
 target   scaffold1    ligand1.1  ligand1.2  ligand1.3
 target   scaffold2    ligand2.1  ligand2.2  ligand2.3
 

in a Molecule[][] array (table):

• table[0]: the table header with Rgroups as 1-atom molecules
• table[i], i > 0: target molecule, scaffold, ligands

If there are more Rgroup ligands with the same rgroup index in the query (e.g. multiple R1 groups) then corresponding ligands will be fused. If there is no Rgroup ligand with an rgroup index then the corresponding table entry is null. If the colorTag is specified then a color map symbol is set in the molecule property for each atom, separated by SEPARATOR characters:

• the least ligand attachment query atom Rgroup index for ligand atoms
• 0 for scaffold atoms

You can run MView with setting atom colors from the SDF tag DMAP, symbol - color pairs given in file Colors.ini:

 mview -t DMAP -p Colors.ini ligands.sdf
 

By default, color map is stored in atom sets which can be written in MRV format and is automatically handled by MView. See MolAtom.getSetSeq(). Rgroups in the table header are represented by any-atoms with rgroup index set in atom map to enable SMILES export.

Parameters:

headerType - is the header type:

• HEADER_NONE for no header
• HEADER_RGROUP for header with rgroup atoms (cannot be exported to SMILES)
• HEADER_MAP for mapped any atoms (for SMILES export)

addCols - additional columns to include:

• COL_MOLECULE for including the target,
• COL_SCAFFOLD for including the scaffold,
• COL_MOLECULE | COL_SCAFFOLD for both,
• 0 for none

colorTag - is the molecule property name for setting the color map null if color should be stored in atomsets

Returns:

the molecule table

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

findLigandTableRow

public Molecule[] findLigandTableRow(int addCols)
                              throws chemaxon.sss.search.SearchException

Returns a ligand table row with ligands corresponding to a the first search hit. Format:

 target    scaffold        ligand R1     ligand R2     ligand R3    ...
 

The target and the scaffold columns are optional. The color map is stored in atom sets which can be written in MRV format and is automatically handled by MView. See MolAtom.getSetSeq(). Attachment points in ligands are represented according to attachment type set in setAttachmentType(int).

Parameters:

addCols - additional columns to include:

• COL_MOLECULE for including the target,
• COL_SCAFFOLD for including the scaffold,
• COL_MOLECULE | COL_SCAFFOLD for both,
• 0 for none

Returns:

the table row

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

findLigandTableRow

public Molecule[] findLigandTableRow(int addCols,
                                     java.lang.String colorTag)
                              throws chemaxon.sss.search.SearchException

Returns a ligand table row with ligands corresponding to a the first search hit. Format:

 target    scaffold        ligand R1     ligand R2     ligand R3    ...
 

The target and the scaffold columns are optional. By default, color map is stored in atom sets which can be written in MRV format and is automatically handled by MView. See MolAtom.getSetSeq(). Attachment points in ligands are represented according to attachment type set in setAttachmentType(int).

Parameters:

addCols - additional columns to include:

• COL_MOLECULE for including the target,
• COL_SCAFFOLD for including the scaffold,
• COL_MOLECULE | COL_SCAFFOLD for both,
• 0 for none

colorTag - is the molecule property name for setting the color map, null if color should be stored in atomsets

Returns:

the table row

Throws:

chemaxon.sss.search.SearchException - on search error

Since:

JChem 5.3

getLigandTableHeader

public Molecule[] getLigandTableHeader(int headerType,
                                       int addCols)

Returns ligand table header. Format:

 query    scaffold        R1         R2         R3    ...
 

The query and the scaffold columns are optional. Color maps are stored in atom sets which can be written in MRV format and is automatically handled by MView. See MolAtom.getSetSeq(). Rgroups in the table header are represented by any-atoms with rgroup index set in atom map or by rgroup atoms.

Parameters:

headerType - is the header type:

• HEADER_RGROUP for header with rgroup atoms (cannot be exported to SMILES)
• HEADER_MAP for mapped any atoms (for SMILES export)

addCols - additional columns to include:

• COL_MOLECULE for including the query,
• COL_SCAFFOLD for including the scaffold,
• COL_MOLECULE | COL_SCAFFOLD for both,
• 0 for none

Since:

JChem 5.1.1

getLigandTableHeader

public Molecule[] getLigandTableHeader(int headerType,
                                       int addCols,
                                       java.lang.String colorTag)

Returns ligand table header. Format:

 query    scaffold        R1         R2         R3    ...
 

The query and the scaffold columns are optional. By default, color map is stored in atom sets which can be written in MRV format and is automatically handled by MView. See MolAtom.getSetSeq(). Rgroups in the table header are represented by any-atoms with rgroup index set in atom map or by rgroup atoms.

Parameters:

headerType - is the header type:

• HEADER_RGROUP for header with rgroup atoms (cannot be exported to SMILES)
• HEADER_MAP for mapped any atoms (for SMILES export)

addCols - additional columns to include:

• COL_MOLECULE for including the query,
• COL_SCAFFOLD for including the scaffold,
• COL_MOLECULE | COL_SCAFFOLD for both,
• 0 for none

colorTag - is the molecule property name for setting the color map, null if color should be stored in atomsets

isLicensed

public boolean isLicensed()

Description copied from class: MolSearch

Gets whether searching is included in the user licence.

Specified by:

isLicensed in interface chemaxon.license.Licensable

Overrides:

isLicensed in class MolSearch

Returns:

true if searching is included in the license, false otherwise

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Description copied from class: MolSearch

Set the license to be used by the search object.

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

Overrides:

setLicenseEnvironment in class MolSearch