Package chemaxon.sss.search
Class StandardizedMolSearch
- java.lang.Object
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- chemaxon.sss.search.Search
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- chemaxon.sss.search.MolSearch
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- chemaxon.sss.search.StandardizedMolSearch
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- All Implemented Interfaces:
chemaxon.license.Licensable
,SearchConstants
,StereoConstants
,SimpleSearcher
@PublicAPI 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
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Field Summary
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Fields inherited from class chemaxon.sss.search.MolSearch
isOrigTargetMayBeMarkush
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Fields inherited from class chemaxon.sss.search.Search
MRV_OUTPUT_LEVEL, preMatchMap, searchOptions
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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
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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_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS
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Constructor Summary
Constructors Constructor Description StandardizedMolSearch()
Constructs a StandardizedMolSearch object.
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Method Summary
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Methods inherited from class chemaxon.sss.search.MolSearch
addComparator, addMatch, addMatch, checkFilter, checkFilter, clearComparators, clearMatch, findAllHits, findFirstHit, findNextHit, getQuery, getSearcher, getTarget, isLicensed, isMatching, removeComparator, setLicenseEnvironment, setOrigTargetMayBeMarkush, setParameters, setQuery, setQuery, setQuery, setSearchOptions, setStandardizer, setTarget, setTarget, setTransformer, stop
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Methods inherited from class chemaxon.sss.search.Search
findAll, findAllGroups, findFirst, findFirstGroup, findNext, findNextGroup, getMatchCount, getQueryAsString, getQueryToPrint, getSearchOptions, getTargetAsString, getTargetToPrint, isMatchCountBetween, isMatchCountInRelation, isMatchCountInRelation, isVerbose, setSearchOptions, setVerbose
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Constructor Detail
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StandardizedMolSearch
public StandardizedMolSearch()
Constructs a StandardizedMolSearch object. Sets general aromatization as standardization. This standardization can be modified throughMolSearch.setStandardizer(chemaxon.standardizer.Standardizer)
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