Stereo specific search options

In this document the stereo search options are summarized and their usage is shown in different search interfaces.

#### Absolute stereo (ignore chiral flag) Sets whether a chiral flag should be ignored or not.	Query	Absolute stereo (query)	Target	Absolute stereo (target)	Hit		---	---	---	---	---			Yes		Yes				No		No
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setQueryAbsoluteStereo( true / false ); searchOptions.setTargetAbsoluteStereo ( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `true` for both options.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setAbsoluteStereo( SearchConstants.ABS_STEREO_TABLE_OPTION / SearchConstants.ABS_STEREO_CHIRAL_FLAG / SearchConstants.ABS_STEREO_ALWAYS_ON ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `SearchConstants.ABS_STEREO_TABLE_OPTION`.JChem Oracle CartridgeUse the jc_compare operator with absoluteStereo:t/c/a option, where: t: (default) do as configured for the table in case of JChem tables or as configured for the index in case of non-JChem tables c: consider chiral flag a: all chiral atoms are absoluteExample: `SELECT count() FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s absoluteStereo:c') = 1;`jcsearch command line toolUse the following command line parameters for memory search: `--queryAbsoluteStereo:y/n`(default:`y`); `--targetAbsoluteStereo:y/n`(default:`y`);while database search accepts the following parameter: `--DBAbsoluteStereo:T/C/A`, where: `T`(default): as set for table in database; `C`: always check chiral flag (false); `A`: always absolute stereo (true).
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Double bond stereo: no check / marked / all double bonds Sets how double bond cis/trans stereo information should match during the search. No check: No double bond cis/trans is considered. Marked: (Default) Double bond cis/trans stereo is checked for double bonds designated by the stereo search flag only. However, for queries coming from the Daylight formats family, all double bonds are considered which have specified stereo configuration. See the matching differences between different formats. * All: All double bonds are checked for cis/trans stereo matching.			Target				---	---	---	---	---		Query	Option						No check						Marked						All
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setDoubleBondStereoMatchingMode( StereoConstants.DBS_NONE /StereoConstants.DBS_MARKED / StereoConstants.DBS_ALL ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions); Default value is StereoConstants.DBS_MARKED JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setDoubleBondStereoMatchingMode( StereoConstants.DBS_NONE /StereoConstants DBS_MARKED / StereoConstants.DBS_ALL ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is StereoConstants.DBS_MARKED JChem Oracle CartridgeUse the jc_compare operator doubleBondStereo:N/M/A, where: N: none; M: marked (default); A: all.Example:`SELECT count() FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s doubleBondStereo:A') = 1;`jcsearch command line toolUse the following command line parameter:`--doubleBondStereo:N/M/A` N: none; M: marked (default); * A: all.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore cumulene or ring cis-trans stereo Sets ignoring cumulene or ring cis-trans stereo information during serching.

#### Ignore cumulene or ring cis-trans stereo Sets ignoring cumulene or ring cis-trans stereo information during serching.
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreCumuleneOrRingCisTransStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `true`.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreCumuleneOrRingCisTransStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `true`. JChem Oracle CartridgeUse the jc_compare operator ignoreCumuleneOrRingCisTransStereo:y/n where: y: yes (default); n: nojcsearch command line toolUse the following command line parameter:`--ignoreCumuleneOrRingCisTransStereo:y/n` y: yes (default); n: no.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreCumuleneOrRingCisTransStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is true.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreCumuleneOrRingCisTransStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is true. JChem Oracle CartridgeUse the jc_compare operator ignoreCumuleneOrRingCisTransStereo:y/n where: y: yes (default); n: nojcsearch command line toolUse the following command line parameter:--ignoreCumuleneOrRingCisTransStereo:y/n y: yes (default); n: no.

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore axial stereo Sets ignoring axial stereo information during searching.

#### Ignore axial stereo Sets ignoring axial stereo information during searching.
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreAxialStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `true`.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreAxialStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `true`. JChem Oracle CartridgeUse the jc_compare operator ignoreAxialStereo:y/n where: y: yes (default); n: nojcsearch command line toolUse the following command line parameter:`--ignoreAxialStereo:y/n` y: yes (default); n: no.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreAxialStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is true.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreAxialStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is true. JChem Oracle CartridgeUse the jc_compare operator ignoreAxialStereo:y/n where: y: yes (default); n: nojcsearch command line toolUse the following command line parameter:--ignoreAxialStereo:y/n y: yes (default); n: no.

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore double bond stereo Sets ignoring double bond stereo information during searching. If this option is set (true) double bond stereo information is ignored and setStereoSearchType(int) only specifies tetrahedral stereo matching.
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreDoubleBondStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `false`.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreDoubleBondStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions); Default value is `false`. JChem Oracle CartridgeUse the jc_compare operator ignoreDoubleBondStereo:y/n where: y: yes; n: no (default)jcsearch command line toolUse the following command line parameter:`--ignoreDoubleBondStereo:y/n` y: yes; n: no (default).
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore double bond stereo Sets ignoring double bond stereo information during searching. If this option is set (true) double bond stereo information is ignored and setStereoSearchType(int) only specifies tetrahedral stereo matching.

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreDoubleBondStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is false.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreDoubleBondStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions); Default value is false. JChem Oracle CartridgeUse the jc_compare operator ignoreDoubleBondStereo:y/n where: y: yes; n: no (default)jcsearch command line toolUse the following command line parameter:--ignoreDoubleBondStereo:y/n y: yes; n: no (default).

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore syn-anti stereo Sets ignoring syn-anti stereo information during searching.

#### Ignore syn-anti stereo Sets ignoring syn-anti stereo information during searching.
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreSynAntiStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `true`. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreSynAntiStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `true`. . JChem Oracle CartridgeUse the jc_compare operator ignoreSynAntiStereo:y/n where: y: yes (default); n: nojcsearch command line toolUse the following command line parameter:`--ignoreSynAntiStereo:y/n` y: yes (default); n: no
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreSynAntiStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is true. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreSynAntiStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is true. . JChem Oracle CartridgeUse the jc_compare operator ignoreSynAntiStereo:y/n where: y: yes (default); n: nojcsearch command line toolUse the following command line parameter:--ignoreSynAntiStereo:y/n y: yes (default); n: no

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore tetrahedral stereo Sets ignoring tetrahedral stereo information during searching. If this option is set (true) tetrahedral stereo information is ignored and setStereoSearchType(int) only specifies double bond stereo matching.
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreTetrahedralStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `false`. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreTetrahedralStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `false`. JChem Oracle CartridgeUse the jc_compare operator ignoreTetrahedralStereo:y/n where: y: yes ; n: no (default)jcsearch command line toolUse the following command line parameter:`--ignoreTetrahedralStereo:y/n` y: yes; n: no (default).
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ignore tetrahedral stereo Sets ignoring tetrahedral stereo information during searching. If this option is set (true) tetrahedral stereo information is ignored and setStereoSearchType(int) only specifies double bond stereo matching.

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreTetrahedralStereo( true / false ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is false. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setIgnoreTetrahedralStereo( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is false. JChem Oracle CartridgeUse the jc_compare operator ignoreTetrahedralStereo:y/n where: y: yes ; n: no (default)jcsearch command line toolUse the following command line parameter:--ignoreTetrahedralStereo:y/n y: yes; n: no (default).

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Stereo search type Specifies the way stereo information is considered during searching. `(setStereoModel(int)`specifies the model for calculating the stereo information.) Stereospecific (default in case of search types other than duplicate): When the query does not contain stereo information, the hits will include results both with and without stereo information. Otherwise, the stereo information is taken into account during the search. Ignore stereo: All stereo information is ignored. Exact stereo (default in case of duplicate search): All stereo information is tested for equality, meaning that a non-stereo query only matches non-stereo targets and enhanced stereo groups can't match on absolute stereo atoms. Diastereomer stereo : Retrieves stereoisomers where tetrahedral stereo information is present on the same stereo centers, but their configuration (parity) is arbitrary. * Enantiomer stereo: Retrieves the given query stereo configuration and its enantiomer as well.
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoSearchType( SearchConstants.STEREO_SPECIFIC / SearchConstants.STEREO_IGNORE / SearchConstants.STEREO_EXACT / SearchConstants.STEREO_DIASTEREOMER / SearchConstants.STEREO_ENANTIOMER ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `SearchConstants.STEREO_SPECIFIC`. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoSearchType( SearchConstants.STEREO_SPECIFIC / SearchConstants.STEREO_IGNORE / SearchConstants.STEREO_EXACT / SearchConstants.STEREO_DIASTEREOMER / SearchConstants.STEREO_ENANTIOMER ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `SearchConstants.STEREO_SPECIFIC`. JChem Oracle CartridgeUse the jc_compare operator with stereoSearchType:s/i/e/d/a s: stereospecific (default); i: ignore stereo; e: exact stereo; d: diastereomer stereo; a: enantomer stereo;Example:`SELECT count() FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s exactStereoMatching:y') = 1;`jcsearch command line toolUse the following command line parameter:`--stereoSearchType:s/i/e/d/a` s: stereospecific (default); i: ignore stereo; e: exact stereo; d: diastereomer stereo; * a: enantomer stereo;
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Stereo search type Specifies the way stereo information is considered during searching. (setStereoModel(int)specifies the model for calculating the stereo information.) Stereospecific (default in case of search types other than duplicate): When the query does not contain stereo information, the hits will include results both with and without stereo information. Otherwise, the stereo information is taken into account during the search. Ignore stereo: All stereo information is ignored. Exact stereo (default in case of duplicate search): All stereo information is tested for equality, meaning that a non-stereo query only matches non-stereo targets and enhanced stereo groups can't match on absolute stereo atoms. Diastereomer stereo : Retrieves stereoisomers where tetrahedral stereo information is present on the same stereo centers, but their configuration (parity) is arbitrary. * Enantiomer stereo: Retrieves the given query stereo configuration and its enantiomer as well.

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoSearchType( SearchConstants.STEREO_SPECIFIC / SearchConstants.STEREO_IGNORE / SearchConstants.STEREO_EXACT / SearchConstants.STEREO_DIASTEREOMER / SearchConstants.STEREO_ENANTIOMER ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is SearchConstants.STEREO_SPECIFIC. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoSearchType( SearchConstants.STEREO_SPECIFIC / SearchConstants.STEREO_IGNORE / SearchConstants.STEREO_EXACT / SearchConstants.STEREO_DIASTEREOMER / SearchConstants.STEREO_ENANTIOMER ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is SearchConstants.STEREO_SPECIFIC. JChem Oracle CartridgeUse the jc_compare operator with stereoSearchType:s/i/e/d/a s: stereospecific (default); i: ignore stereo; e: exact stereo; d: diastereomer stereo; a: enantomer stereo;Example:`SELECT count() FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s exactStereoMatching:y') = 1;jcsearch command line toolUse the following command line parameter:--stereoSearchType:s/i/e/d/a` s: stereospecific (default); i: ignore stereo; e: exact stereo; d: diastereomer stereo; * a: enantomer stereo;

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Stereo model Sets stereo model option. Stereo models describe search strategies in cases of molecules with defined stereochemistry. See details and examples... Local: Default for markush search in all cases and for non-markush duplicate search in query tables. Global: Default for non-markush duplicate search (with the exception of query tables). * Comprehensive: Default otherwise
MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoModel( SearchConstants.STEREO_MODEL_LOCAL / SearchConstants.STEREO_MODEL_COMPREHENSIVE / SearchConstants.STEREO_MODEL_GLOBAL / SearchConstants.STEREO_MODEL_DEFAULT ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is `SearchConstants.STEREO_MODEL_DEFAULT`, whose actual behavior depends on the search type. For substructure and superstructure searches, it equals to `SearchConstants.STEREO_MODEL_COMPREHENSIVE`, while for other searches, it usually equals to `SearchConstants.STEREO_MODEL_GLOBAL`.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoModel( SearchConstants.STEREO_MODEL_LOCAL / SearchConstants.STEREO_MODEL_COMPREHENSIVE / SearchConstants.STEREO_MODEL_GLOBAL / SearchConstants.STEREO_MODEL_DEFAULT ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is `SearchConstants.STEREO_MODEL_DEFAULT`, whose actual behavior depends on the search type and the type of the structure table. For substructure and superstructure searches, it equals to `SearchConstants.STEREO_MODEL_COMPREHENSIVE`, while for other searches, it usually equals to `SearchConstants.STEREO_MODEL_GLOBAL`. JChem Oracle CartridgeUse the jc_compare operator with stereoModel:l/g/c l: local stereo model; g: global stereo model; c: comprehensive stereo model;jcsearch command line toolUse the following command line parameter:`--stereoModel:d/l/g/c` d: default; l: local; g: global; * c: comprehensive.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Stereo model Sets stereo model option. Stereo models describe search strategies in cases of molecules with defined stereochemistry. See details and examples... Local: Default for markush search in all cases and for non-markush duplicate search in query tables. Global: Default for non-markush duplicate search (with the exception of query tables). * Comprehensive: Default otherwise

MolSearch API MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoModel( SearchConstants.STEREO_MODEL_LOCAL / SearchConstants.STEREO_MODEL_COMPREHENSIVE / SearchConstants.STEREO_MODEL_GLOBAL / SearchConstants.STEREO_MODEL_DEFAULT ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);Default value is SearchConstants.STEREO_MODEL_DEFAULT, whose actual behavior depends on the search type. For substructure and superstructure searches, it equals to SearchConstants.STEREO_MODEL_COMPREHENSIVE, while for other searches, it usually equals to SearchConstants.STEREO_MODEL_GLOBAL.JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setStereoModel( SearchConstants.STEREO_MODEL_LOCAL / SearchConstants.STEREO_MODEL_COMPREHENSIVE / SearchConstants.STEREO_MODEL_GLOBAL / SearchConstants.STEREO_MODEL_DEFAULT ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);Default value is SearchConstants.STEREO_MODEL_DEFAULT, whose actual behavior depends on the search type and the type of the structure table. For substructure and superstructure searches, it equals to SearchConstants.STEREO_MODEL_COMPREHENSIVE, while for other searches, it usually equals to SearchConstants.STEREO_MODEL_GLOBAL. JChem Oracle CartridgeUse the jc_compare operator with stereoModel:l/g/c l: local stereo model; g: global stereo model; c: comprehensive stereo model;jcsearch command line toolUse the following command line parameter:--stereoModel:d/l/g/c d: default; l: local; g: global; * c: comprehensive.

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home