Resultset specific search options

findAll():

        MolSearch searcher = new MolSearch();
        // ...
        int[][] hits = searcher.findAll();

or findFirst() and consecutive findNext() calls:

        MolSearch searcher = new MolSearch();
        // ...
        List<int[]> hits = new ArrayList<int[]>();
        int[] hit = searcher.findFirst();
        while (hit != null) {
            hits.add(hit);
            hit = searcher.findNext();
        }

Not applicable.

Not applicable.

Use the following command line parameter:
--allHits
Instead of checking the existence of matching, all matchings of the query molecule(s) are reported.

Not applicable.

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

Use the jc_compare operator as jc_compare()...)=0

As jc_compare compares molecules or reactions and reports a match by returning 1 or an unmatch by returning 0.
(For selecting non-matching targets in domain index scans, the earlyResults option must be set to '0'.)

jc_compare (target_structure IN VARCHAR2/CLOB/BLOB, query_structure IN VARCHAR2/CLOB/BLOB, options IN VARCHAR2) = 1/0;

Use the following command line parameter:

-n
List non-hits. For using with multiple targets, see options --and and --or.

Not applicable.

Not applicable.

Not applicable.

Use the following command line parameter:
--and
If used together with option -n, a hit is returned if none of the query molecules match.

Not applicable.

Not applicable.

 The search is performed for each individual query structure and the union of the hits is returned. See description of possibilities of concatenated queries.

Use the following command line parameter:

--or

If used together with option -n, a hit is returned if at least one query molecules does not match.

Not applicable.

        JChemSearch searcher = new JChemSearch();
        searcher.setOrder( JChemSearch.NO_ORDERING /
                JChemSearch.ORDERING_BY_ID / JChemSearch.ORDERING_BY_ID_OR_SIMILARITY /
                JChemSearch.ORDERING_BY_FILTER_ID_LIST );

Default value is ORDERING_BY_ID_OR_SIMILARITY.

 Not applicable.

Not applicable.