Atomproperty specific search options

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

Charge matching mode

Specifies charge searching behavior. See examples... The following options are available:

  • Default or On: charged query matches only charged target, noncharged query matches all;

  • Exact: charged query matches only charged target, noncharged query matches only noncharged target;

  • Ignore: both charged and noncharged query matches charged and noncharged target as well.

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setChargeMatching( SearchConstants.CHARGE_MATCHING_DEFAULT /
SearchConstants.CHARGE_MATCHING_EXACT / SearchConstants.CHARGE_MATCHING_IGNORE );
// ...
MolSearch searcher = new MolSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.CHARGE_MATCHING_DEFAULT.
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setChargeMatching( SearchConstants.CHARGE_MATCHING_DEFAULT /
SearchConstants.CHARGE_MATCHING_EXACT / SearchConstants.CHARGE_MATCHING_IGNORE );
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.CHARGE_MATCHING_DEFAULT.
JChem Oracle Cartridge
Use the jc_compare operator with charge:d/e/i, where:
 
d: default
e: exact
i: ignore (forces implicitHMatching:i in case of duplicate search)
 
Example: SELECT count(*) FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s charge:e') = 1;
jcsearch command line tool
Use the following command line parameter:
 
--charge:d/e/i
 
d: default;
e: exact;
i: ignore (forces --implicitHMatching:i in case of duplicate search).

Isotope matching mode

Specifies isotope searching behavior. See examples... The following options are available:

  • Default and On: isotope query matches only isotope target, non-isotope query matches all;

  • Exact: isotope query matches only isotope target, non-isotope query matches only non-isotope target;

  • Ignore: both isotope and non-isotope query matches isotope and non-isotope target as well.

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setIsotopeMatching( SearchConstants.ISOTOPE_MATCHING_DEFAULT /
SearchConstants.ISOTOPE_MATCHING_EXACT / SearchConstants.ISOTOPE_MATCHING_IGNORE );
// ...
MolSearch searcher = new MolSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.ISOTOPE_MATCHING_DEFAULT.
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setIsotopeMatching( SearchConstants.ISOTOPE_MATCHING_DEFAULT /
SearchConstants.ISOTOPE_MATCHING_EXACT / SearchConstants.ISOTOPE_MATCHING_IGNORE );
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.ISOTOPE_MATCHING_DEFAULT.
JChem Oracle Cartridge
Use the jc_compare operator with isotope:d/e/i, where:
 
d: default
e: exact
i: ignore
 
Example: SELECT count(*) FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s isotope:e') = 1;
jcsearch command line tool
Use the following command line parameter:
 
--isotope:d/e/i
 
d: default;
e: exact;
i: ignore

Radical matching mode

Specifies radical searching behavior. See examples... The following options are available:

  • Default and On: radical query matches only radical target, non-radical query matches all;

  • Exact: radical query matches only radical target, non-radical query matches only non-radical target;

  • Ignore: both radical and non-radical query matches radical and non-radical target as well.

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setRadicalMatching( SearchConstants.RADICAL_MATCHING_DEFAULT /
SearchConstants.RADICAL_MATCHING_EXACT / SearchConstants.RADICAL_MATCHING_IGNORE );
// ...
MolSearch searcher = new MolSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.RADICAL_MATCHING_DEFAULT.
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setRadicalMatching( SearchConstants.RADICAL_MATCHING_DEFAULT /
SearchConstants.RADICAL_MATCHING_EXACT / SearchConstants.RADICAL_MATCHING_IGNORE );
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.RADICAL_MATCHING_DEFAULT.
JChem Oracle Cartridge
Use the jc_compare operator with radical:d/e/i, where:
 
d: default
e: exact
i: ignore
 
Example: SELECT count(*) FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s radical:i') = 1;
jcsearch command line tool
Use the following command line parameter:
 
--radical:d/e/i
 
d: default;
e: exact;
i: ignore

Valence matching mode

Specifies valence searching behavior. The following options are available:

  • True (default): valence should be checked during search;

  • Ignore: valence check should be ignored.

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setValenceMatching(
SearchConstants.VALENCE_MATCHING_ON / SearchConstants.VALENCE_MATCHING_IGNORE );
// ...
MolSearch searcher = new MolSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants.VALENCE_MATCHING_ON.
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setValenceMatching(
SearchConstants.VALENCE_MATCHING_ON / SearchConstants.VALENCE_MATCHING_IGNORE );
 
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is SearchConstants. VALENCE_MATCHING_ON.
JChem Oracle Cartridge
Use the jc_compare operator with valence:d/i
jcsearch command line tool
Use the following command line parameter:
 
--valence:d/i
 
d: default;
i: ignore

Sp hybridization state checking

Sets whether the sp-hybridization state of the atoms should be considered. If true the sp-hybridization state is checked. Default value is false.
See detailed description of calculation of the sp-hybridization state and search examples with sp-hyridization checking.

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setCheckSpHyb( true / false );
// ...
MolSearch searcher = new MolSearch();
searcher.setSearchOptions(searchOptions);
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setCheckSpHyb( true / false );
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
JChem Oracle Cartridge
Use the jc_compare operator with checkSpHyb:Y/N.
jcsearch command line tool
Use the following command line parameter:
--checkSpHyb:y/n