chemaxon.sss.search
Class StandardizedMolSearch

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

All Implemented Interfaces:

chemaxon.license.Licensable, SearchConstants, StereoConstants

Direct Known Subclasses:

RGroupDecomposition

public class StandardizedMolSearch
extends MolSearch

MolSearch subclass that standardizes (e.g. aromatizes) query and target structures before searching. The query and target molecules are cloned before standardization, so the original objects are not modified during the use of this class.

Since:

JChem 3.2

Author:

Szabolcs Csepregi Date: Aug 17, 2006

Field Summary

Fields inherited from class chemaxon.sss.search.MolSearch

groupHit, groupHitHandler, isOrigTargetMayBeMarkush, isQueryStandardizable, isTargetStandardizable

Fields inherited from class chemaxon.sss.search.Search

preMatchLength, preMatchQueryAtoms, preMatchTargetAtoms, searchOptions

Fields inherited from interface chemaxon.struc.StereoConstants

ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, 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_SIMILARITY_THRESHOLD, DISSIMILARITY, DUPLICATE, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, KEEP_QUERY_ORDER, MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_DISABLED, MARKUSH_ENABLED, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, MIX_SGROUP_MATCHING_OFF, MIX_SGROUP_MATCHING_ON, NO_ABAS, NO_SCREEN, OPTION_CHARGE_MATCHING, OPTION_EXACT_FRAGMENT, OPTION_ISOTOPE_MATCHING, OPTION_KEEP_QUERY_ORDER, OPTION_MARKUSH_AROM, OPTION_MARKUSH_ENABLED, OPTION_MARKUSH_HIT, OPTION_MIX_SGROUP_MATCHING, OPTION_RADICAL_MATCHING, OPTION_STEREO_MODEL, OPTION_TAUTOMER_SEARCH, OPTION_VAGUE_BOND, OPTION_VALENCE_MATCHING, PERFECT, R_NODE_PLACEHOLDER, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, REARRANGE_QUERY, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_DIASTEREOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, 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, VALENCE_MATCHING_IGNORE, VALENCE_MATCHING_ON

Constructor Summary

StandardizedMolSearch()
Constructs a StandardizedMolSearch object.

Method Summary

void	setStandardizer(Standardizer st, boolean bq, boolean bt) Sets standardizer object of this MolSearch class, to be used for the query and target molecules, Chemical Terms configuration and re-standardization of query tautomers at tautomer searching.

Methods inherited from class chemaxon.sss.search.MolSearch

addComparator, addMatch, addMatch, checkFilter, checkFilter, clearComparators, clearMatch, filter, findAll, findAllGroups, findAllOrder, findFirst, findFirstGroup, findNext, findNextGroup, getFilter, getGroupHit, getMatchingQuery, getMatchingTarget, getMolecule, getQuery, getQueryStructure, getTarget, hasFilter, hasHitFilter, isLicensed, isMatching, keepGroupOrder, removeComparator, setFilter, setFilterConfig, setFilterConfig, setHitIncludesRNodes, setLicenseEnvironment, setMolecule, setOrigTargetMayBeMarkush, setQuery, setQuery, setQuery, setQueryStructure, setSearchOptions, setTarget, setTarget, stop

Methods inherited from class chemaxon.sss.search.Search

areMatchingBondTypes, areMatchingBondTypes, getAtomStereo, getDefaultUndefinedRAtom, getDoubleBondStereoMatchingMode, getHCountMatching, getMatchCount, getOption, getQueryAsString, getQueryToPrint, getSearchOptions, getSearchType, getTargetAsString, getTargetToPrint, isExactAtomMatching, isExactBondMatching, isExactChargeMatching, isExactIsotopeMatching, isExactQueryAtomMatching, isExactRadicalMatching, isExactStereoMatching, isMatchCountBetween, isMatchCountInRelation, isOrderSensitiveSearch, isPerfectSearchType, isQueryAbsoluteStereo, isSubgraphSearch, isTargetAbsoluteStereo, isTautomerSearch, isVerbose, setDoubleBondStereoMatchingMode, setExactAtomMatching, setExactBondMatching, setExactChargeMatching, setExactIsotopeMatching, setExactQueryAtomMatching, setExactRadicalMatching, setExactStereoMatching, setHCountMatching, setOption, setOptions, setOrderSensitiveSearch, setQueryAbsoluteStereo, setSearchOptions, setSearchType, setStereoCareChecking, setStereoSearch, setSubgraphSearch, setTargetAbsoluteStereo, setTautomerSearch, setVerbose

Methods inherited from class java.lang.Object

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

Constructor Detail

StandardizedMolSearch

public StandardizedMolSearch()

Constructs a StandardizedMolSearch object.

Method Detail

setStandardizer

public void setStandardizer(Standardizer st,
                            boolean bq,
                            boolean bt)

Sets standardizer object of this MolSearch class, to be used for the query and target molecules, Chemical Terms configuration and re-standardization of query tautomers at tautomer searching. Default is aromatization only.

Overrides:

setStandardizer in class MolSearch

Parameters:

st - Standardizer object. null means default (aromatization). WARNING: Standardization that changes atom indexes is not supported!

bq - if false, standardization is not done on query. (Useful if query is already standardized.)

bt - if false, standardization is not done on target. (Useful if target is already standardized.)

Since:

JChem 3.2