Package chemaxon.search

Class StandardizedMolSearch

java.lang.Object

chemaxon.search.AbstractSearch

chemaxon.search.MolSearch

chemaxon.search.StandardizedMolSearch

All Implemented Interfaces:

Licensable, SearchConstants, StereoConstants

Direct Known Subclasses:

RgroupDecomposition

@PublicApi
public class StandardizedMolSearch
extends MolSearch

MolSearch subclass that standardizes query and target structures by default before searching.

The default standardization action is general aromatization. It can be customized using MolSearch.setStandardizer(chemaxon.standardizer.Standardizer). The input molecules are cloned before standardization, so the original objects are not modified during the use of this class.

Since:

JChem 3.2

Field Summary

Fields inherited from class chemaxon.search.MolSearch

isOrigTargetMayBeMarkush

Fields inherited from class chemaxon.search.AbstractSearch

MRV_OUTPUT_LEVEL, preMatchMap, searchOptions

Fields inherited from interface chemaxon.search.api.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_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

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

Constructor Summary

Constructors

Constructor	Description
StandardizedMolSearch()	Constructs a StandardizedMolSearch object.

Method Summary

Methods inherited from class chemaxon.search.MolSearch

addComparator, addMatch, addMatch, checkFilter, checkFilter, clearComparators, clearMatch, findAllHits, findFirstHit, findNextHit, getQuery, getTarget, isLicensed, isMatching, removeComparator, setLicenseEnvironment, setOrigTargetMayBeMarkush, setParameters, setQuery, setQuery, setQuery, setSearchOptions, setStandardizer, setTarget, setTarget, stop

Methods inherited from class chemaxon.search.AbstractSearch

findAll, findAllGroups, findFirst, findFirstGroup, findNext, findNextGroup, getMatchCount, getQueryToPrint, getSearchOptions, getTargetToPrint, isMatchCountBetween, isMatchCountInRelation, isVerbose, setSearchOptions, setVerbose

Methods inherited from class java.lang.Object

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

Constructor Details

StandardizedMolSearch

public StandardizedMolSearch()

Constructs a StandardizedMolSearch object. Sets general aromatization as standardization. This standardization can be modified through MolSearch.setStandardizer(chemaxon.standardizer.Standardizer).