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Resultset specific search options

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

Enumeration of all query-target mappings

Determines whether a target structure contains a query structure. Specifies the matching atoms in the target structure in the order of the corresponding query atoms.
MolSearch API

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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();
        }

JChemSearch API

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Not applicable.

JChem Oracle Cartridge

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Not applicable.

jcsearch command line tool

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

Inverse hit list

Determines if the inverse of the hitset should be returned. Default value is false.
MolSearch API

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Not applicable.

JChemSearch API

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

JChem Oracle Cartridge

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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;

jcsearch command line tool

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Use the following command line parameter:

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

Multiple queries (in "and" relation)

If two or more queries are present, all are required to match (default).
MolSearch API

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Not applicable.

JChemSearch API

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Not applicable.

JChem Oracle Cartridge

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Not applicable.

jcsearch command line tool

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

Multiple queries (in "or" relation)

If more than one queries are present, at least one is required to match.
MolSearch API

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Not applicable.

JChemSearch API

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Not applicable.

JChem Oracle Cartridge

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

jcsearch command line tool

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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.

Ordering of results

Sets order property. Determines the order of the result.
MolSearch API

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Not applicable.

JChemSearch API

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        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.

JChem Oracle Cartridge

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 Not applicable.

jcsearch command line tool

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Not applicable.