Absolute stereo (ignore chiral flag)

Sets whether a chiral flag should be ignored or not.

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 Cartridge

Use 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 absolute

Example: SELECT count(*) FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s absoluteStereo:c') = 1;

jcsearch command line tool

Use 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).

Java Server PagesOption can be set on Query>advanced options tab by adding Additional Cartridge-style search option: absoluteStereo:t/c/a.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

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 /StereoConstantsDBS_MARKED / StereoConstants.DBS_ALL );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

Default value is StereoConstants.DBS_MARKED

JChem Oracle Cartridge

Use 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 tool

Use the following command line parameter:--doubleBondStereo:N/M/A

• N: none;

• M: marked (default);

• A: all.

Java Server Pages

Option can be set on Query>advanced options tab by selecting Double bond stereo check: "All", "Marked", and "Off" in the Stereochemisty panel. Default value is "Marked".

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Ignore cumulene or ring cis-trans stereo

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 Cartridge

Use the jc_compare operator ignoreCumuleneOrRingCisTransStereo:y/n where:

• y: yes (default);

• n: no

jcsearch command line tool

Use the following command line parameter:

--ignoreCumuleneOrRingCisTransStereo:y/n

• y: yes (default);

• n: no.

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Ignore axial stereo

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 Cartridge

Use the jc_compare operator ignoreAxialStereo:y/n where:

• y: yes (default);

• n: no

jcsearch command line tool

Use the following command line parameter:

--ignoreAxialStereo:y/n

• y: yes (default);

• n: no.

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Ignore double bond stereo

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 Cartridge

Use the jc_compare operator ignoreDoubleBondStereo:y/n where:

• y: yes;

• n: no (default)

jcsearch command line tool

Use the following command line parameter:--ignoreDoubleBondStereo:y/n

• y: yes;

• n: no (default).

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Ignore syn-anti stereo

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 Cartridge

Use the jc_compare operator ignoreSynAntiStereo:y/n where:

• y: yes (default);

• n: no

jcsearch command line tool

Use the following command line parameter:

--ignoreSynAntiStereo:y/n

• y: yes (default);

• n: no

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Ignore tetrahedral stereo

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 Cartridge

Use the jc_compare operator ignoreTetrahedralStereo:y/n where:

• y: yes ;

• n: no (default)

jcsearch command line tool

Use the following command line parameter:--ignoreTetrahedralStereo:y/n

• y: yes;

• n: no (default).

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Stereo search type

• 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 tool

Use 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;

Java Server Pages

Option can be set on Query>advanced options tab by selecting "On", "Exact", "Diastereomers", or "Off" in the Stereochemisty panel. Default value is "On".

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus

Stereo model

• 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 tool

Use the following command line parameter:--stereoModel:d/l/g/c

• d: default;

• l: local;

• g: global;

• c: comprehensive.

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus