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
Inverse hit list
Multiple queries (in "and" relation)
Multiple queries (in "or" relation)

Ordering of results

#### 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.

#### 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[findAll()](http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/sss/search/Search.html#findAll()): MolSearch searcher = new MolSearch(); // ... int[][] hits = searcher.findAll();or [findFirst()](http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/sss/search/Search.html#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 APINot applicable. JChem Oracle CartridgeNot applicable. jcsearch command line toolUse the following command line parameter:`--allHits` Instead of checking the existence of matching, all matchings of the query molecule(s) are reported.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

MolSearch API[findAll()](http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/sss/search/Search.html#findAll()): MolSearch searcher = new MolSearch(); // ... int[][] hits = searcher.findAll();or [findFirst()](http://www.chemaxon.com/jchem/doc/dev/java/api/chemaxon/sss/search/Search.html#findFirst()) and consecutivefindNext()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 APINot applicable. JChem Oracle CartridgeNot applicable. jcsearch command line toolUse the following command line parameter:--allHits Instead of checking the existence of matching, all matchings of the query molecule(s) are reported.

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Inverse hit list Determines if the inverse of the hitset should be returned. Default value is `false`.
MolSearch APINot applicable. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setReturnsNonHits ( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);JChem Oracle CartridgeUse the jc_compare operator as jc_compare()...)=0As 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 toolUse the following command line parameter:`-n`List non-hits. For using with multiple targets, see options `--and` and `--or`.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Inverse hit list Determines if the inverse of the hitset should be returned. Default value is false.

MolSearch APINot applicable. JChemSearch API JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE); searchOptions.setReturnsNonHits ( true / false ); // ... JChemSearch searcher = new JChemSearch(); searcher.setSearchOptions(searchOptions);JChem Oracle CartridgeUse the jc_compare operator as jc_compare()...)=0As 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 toolUse the following command line parameter:-nList non-hits. For using with multiple targets, see options --and and --or.

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Multiple queries (in "and" relation) If two or more queries are present, all are required to match (default).
MolSearch APINot applicable. JChemSearch APINot applicable. JChem Oracle CartridgeNot applicable. jcsearch command line toolUse the following command line parameter:`--and` If used together with option `-n`, a hit is returned if none of the query molecules match.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Multiple queries (in "or" relation) If more than one queries are present, at least one is required to match.

#### Multiple queries (in "or" relation) If more than one queries are present, at least one is required to match.
MolSearch APINot applicable. JChemSearch APINot applicable. JChem Oracle CartridgeThe 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 toolUse 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.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

MolSearch APINot applicable. JChemSearch APINot applicable. JChem Oracle CartridgeThe 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 toolUse the following command line parameter:--orIf used together with option -n, a hit is returned if at least one query molecules does not match.

See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home

#### Ordering of results Sets order property. Determines the order of the result.
MolSearch APINot applicable. JChemSearch API 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 CartridgeNot applicable.jcsearch command line toolNot applicable.
See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home