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

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);

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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

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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.