Bond specific search options

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

Exact bond matching

Specifies whether bond types should match exactly. If set to true, bond types must match exactly. For example "single or double" matches only "single or double", but matches neither "single" nor "double". Default value is falseor n in case of all search types except duplicate search. MolSearch API


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

JChemSearch API


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

JChem Oracle Cartridge


Use the jc_compare operator with exactBondMatching:y/n.

jcsearch command line tool


Use the following command line parameter:

--exactBondMatching:y/n

Vague bond search levels

This option gives the opportunity of less strict evaluation of query bonds. See the details of vague bond search here. MolSearch API


        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setVagueBondLevel( SearchConstants.VAGUE_BOND_OFF / SearchConstants.VAGUE_BOND_HALF / SearchConstants.VAGUE_BOND_LEVEL1/
                SearchConstants.VAGUE_BOND_LEVEL2 / SearchConstants.VAGUE_BOND_LEVEL3 / SearchConstants.VAGUE_BOND_LEVEL4 );
        // ...
        MolSearch searcher = new MolSearch();
        searcher.setSearchOptions(searchOptions);

JChemSearch API


       JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
        searchOptions.setVagueBondLevel( SearchConstants.VAGUE_BOND_OFF / SearchConstants.VAGUE_BOND_HALF /SearchConstants.VAGUE_BOND_LEVEL1 /
                SearchConstants.VAGUE_BOND_LEVEL2 / SearchConstants.VAGUE_BOND_LEVEL3 / SearchConstants.VAGUE_BOND_LEVEL4 );
        // ...
        JChemSearch searcher = new JChemSearch();
        searcher.setSearchOptions(searchOptions);

JChem Oracle Cartridge


Use the jc_compare operator with vagueBond:n/h/1/2/3/4

    n: off
    h: handling of certain 5-membered ambiguous aromatic rings like [C,N]1C=CC=C1 (default from version 15.9.14);
    1: handling of certain 5-membered ambiguous aromatic rings like [C,N]1C=CC=C1 and 1-atom-long aromatic ring ligands and bridging bonds between two aromatic rings (default in versions prior to 15.9.14);
    2: all single and double ring bonds match aromatic;
    3: all single and double bonds match aromatic;
    4: ignore all bond types.

jcsearch command line tool


Use the following command line parameter:

--vagueBond:n/h/1/2/3/4

    n: off
    h: handling of certain 5-membered ambiguous aromatic rings like [C,N]1C=CC=C1 (default from version 15.9.14);
    1: handling of certain 5-membered ambiguous aromatic rings like [C,N]1C=CC=C1 and 1-atom-long aromatic ring ligands and bridging bonds between two aromatic rings (default in versions prior to 15.9.14);
    2: all single and double ring bonds match aromatic;
    3: all single and double bonds match aromatic;
    4: ignore all bond types.