Polymers and bracket components - search options¶

In this document the search options concerning polymers and bracket components are summarized and their usage is shown in different search interfaces.

Copolymer matching

Ignore mixture brackets

Ignore polymer brackets

Polymer end group matching

Polymer phase-shift

Transform monomer representation

Copolymer matching¶

Adjusts copolymer matching mode. If y(yes)/true then target polymers in copolymers can only be matched by query polymers in copolymers. Default value is n (no)/false.
MolSearch API

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

JChemSearch API

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

JChem Oracle Cartridge

Use the jc_compare operator with copolymerMatching:y/n

jcsearch command line tool

Use the following command line parameter:

--copolymerMatching:y/n

Ignore mixture brackets¶

Adjusts mixture matching. True - if COM, MIX and FOR sgroups should be considered during search. Default value is true.
MolSearch API

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

Default value is true.

JChemSearch API

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

Default value is true

JChem Oracle Cartridge

Use the jc_compare operator with mix:d/i,
which specifies whether COM, MIX and FOR sgroups should be considered during search.

    d (default): do consider;
    i: ignore.

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

jcsearch command line tool

Use the following command line parameter:

--mix:d/i , where

    d: default;
    i: ignore brackets.

Ignore polymer brackets¶

Adjusts polymer matching. True - if polymer sgroups should be considered during search. Default value is true.
MolSearch API

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

JChemSearch API

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

JChem Oracle Cartridge

Use the jc_compare operator with polymer:d/i.

    d (default): do consider;
    i: ignore polymer brackets.

jcsearch command line tool

Use the following command line parameter:

--polymer:d/i, where

    d: default;
    i: ignore brackets.

Polymer end group matching¶

Adjusts polymer end group matching. True - if polymer end groups should be matched during search. In this case the star atom can't match on a specified end group.

Default value is true. See examples here.
MolSearch API

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

JChemSearch API

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

JChem Oracle Cartridge

Use the jc_compare operator with endGroupMatching:y/n.

    yes (default);
    n: no.

jcsearch command line tool

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

    y: yes (default);
    n: no

Polymer phase-shift¶

Adjusts if the phase shifted polymer should match on the original. True if the phase shifted should be matching; false otherwise. Default value is true. See examples here.
MolSearch API

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

JChemSearch API

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

JChem Oracle Cartridge

Use the jc_compare operator with phaseShift:y/n.

    yes (default);
    n: no

jcsearch command line tool

Use the following command line parameter:

--phaseShift:y/n

    y: yes (default);
    n: no

Transform monomer representation¶

Adjusts if monomers should be transformed to structural repeating units if the monomer is polymerizable. Polymers in their source based representation
are transformed to structure based representation. True - if monomers should be transformed, false otherwise. Default value is true. See examples here.
MolSearch API

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

JChemSearch API

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

JChem Oracle Cartridge

Use the jc_compare operator with transformMonomer:y/n

    yes (default);
    n: no.

jcsearch command line tool

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

    y: yes (default);
    n: no.