Homology narrow translation

This option relates to query-side homology handling. The homology narrow translation option can switch off special handling of homology groups, hence they can match the homology group of the same type only (e.g. alkyl on alkyl or chk). The option can have the following values:

• ALL/a: All atoms can have translation.

• MARKED/m: Only marked atoms can have translation. (Not implemented yet.)

• NONE/n: No atom can have translation.

Limitations:

• If homology narrow translation is allowed than query side homology against Markush targets is limited to those cases when Markush targets do not contain any other Markush features than the same homology group as the guery structure does.

• Properties of homology groups (e.g. LO, MID, HI on alkyl) are ignored when both the query and the target structure contains the homology group.

• Rgroups with more than two attachment points are not supported on the query side.

More information about translation options can be found in the Markush search documentation.

MolSearch API

        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setHomologyNarrowTranslation( HomologyTranslationOption.NONE /HomologyTranslationOption.ALL / HomologyTranslationOption.MARKED );
        // ...
        MolSearch searcher = new MolSearch();        searcher.setSearchOptions(searchOptions);

Default value is HomologyTranslationOption.MARKED, but it is not implemented yet and works as HomologyTranslationOption.NONE.

JChemSearch API

        JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setHomologyNarrowTranslation( HomologyTranslationOption.NONE /HomologyTranslationOption.ALL / HomologyTranslationOption.MARKED );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

Default value is HomologyTranslationOption.MARKED, but it is not implemented yet and works as HomologyTranslationOption.NONE.

JChem Oracle Cartridge

Use the jc_compare operator with homologyNarrowTranslation:n/a/m

jcsearch command line tool

Use the following command line parameter:

--homologyNarrowTranslation:n/a/m

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

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite

Homology broad translation

• ALL/a: all query atoms can match on broader homology atoms, if the properties of the group are fulfilled.

• MARKED/m: only the marked query atoms can match on broader homology groups. This option is not yet implemented it works as none.

• NONE/n: no query atoms can match on broader groups, they can only match if the query atom is a homology atom of the same group.

Default value is NONE. Further properties of translation NONE behavior:

• homology groups cannot match and cannot be matched by specific atoms or homology groups being a superset or a subset of the given group;

• homology groups can match pseudo atoms with alias name of the given group (e.g. chk matches alkyl);

• homology properties are ignored (alkyl,LO matches alkyl,HI).

Read more about homology groups.

MolSearch API

        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setHomologyBroadTranslation( HomologyTranslationOption.NONE /HomologyTranslationOption.ALL / HomologyTranslationOption.MARKED );
        // ...
        MolSearch searcher = new MolSearch();
        searcher.setSearchOptions(searchOptions);

Default value is HomologyTranslationOption.MARKED, but it is not implemented yet and works as HomologyTranslationOption.NONE.

JChemSearch API

        JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setHomologyBroadTranslation( HomologyTranslationOption.NONE /HomologyTranslationOption.ALL / HomologyTranslationOption.MARKED );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

Default value is HomologyTranslationOption.MARKED, but it is not implemented yet and works as HomologyTranslationOption.NONE.

JChem Oracle CartridgeUse the jc_compare operator with homologyBroadTranslation:n/a/m

jcsearch command line tool

Use the following command line parameter:--homologyBroadTranslation:n/a/m

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

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite

Markush search enable/disable

MolSearch API

        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setMarkushEnabled( true / false );
        // ...
        MolSearch searcher = new MolSearch();
        searcher.setSearchOptions(searchOptions);

JChemSearch APICannot be set. Depends on database table type.

JChem Oracle CartridgeNot applicable.

jcsearch command line tool

Use the following command line parameter:

--markush:n/y

Default value is n.

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite

Complete homology groups

MolSearch API

        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setCompleteHG( true / false );
        // ...
        MolSearch searcher = new MolSearch();
        searcher.setSearchOptions(searchOptions);

Default value is true.

JChemSearch API

        JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setCompleteHG( true / false );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

Default value is true.

JChem Oracle Cartridge

Use the jc_compare operator with completeHG:y/n

jcsearch command line tool

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

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite

Markush screening

MolSearch APINot applicable.

JChemSearch API

        JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setMarkushScreeningEnabled( true / false );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

Default value is true.

JChem Oracle CartridgeNot applicable.

jcsearch command line tool

Use the following command line parameter:

--markushScreening:y/n

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite

Markush fingerprint screening

MolSearch APINot applicable.

JChemSearch API

        JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setMarkushFPScreeningEnabled( true / false );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

JChem Oracle CartridgeNot applicable.

jcsearch command line tool Not applicable

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite

Hit-index type

MolSearch API

        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setHitIndexType( SearchConstants.MARKUSH_HIT_ORIGINAL / SearchConstants.MARKUSH_HIT_INNER );
        // ...
        MolSearch searcher = new MolSearch();
        searcher.setSearchOptions(searchOptions);

Default value is SearchConstants.MARKUSH_HIT_ORIGINAL.

JChemSearch APINot applicable.

JChem Oracle CartridgeNot applicable.

jcsearch command line tool

Use the following command line parameter:

--hitIndexType:m/i

• m: (default) returns hits for the original Markush diagram;

• i: (default) returns hits for the inner compiled representation.

Java Server PagesNot applicable.

See the availability of the option in further ChemAxon products:

• InstantJChem

• JChem for Excel

• Plexus Suite