In this document the search options concerning atom propeties are summarized and their usage is shown in different search interfaces.
Sp-hybridization state checking
| #### 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. |
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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 CartridgeUse 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 toolUse the following command line parameter:--charge:d/e/i` d: default; e: exact; * i: ignore (forces --implicitHMatching:i in case of duplicate search). |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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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 CartridgeUse the jc_compare operator with isotope:d/e/i, where: d: default e: exact i: ignoreExample: `SELECT count() FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s isotope:e') = 1;jcsearch command line toolUse the following command line parameter:--isotope:d/e/i` d: default; e: exact; * i: ignore |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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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 CartridgeUse the jc_compare operator with radical:d/e/i, where: d: default e: exact i: ignoreExample: `SELECT count() FROM nci_150k WHERE jc_compare(structure, 'Brc1ccccc1', 't:s radical:i') = 1;jcsearch command line toolUse the following command line parameter:--radical:d/e/i` d: default; e: exact; * i: ignore |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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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 CartridgeUse the jc_compare operator with valence:d/ijcsearch command line toolUse the following command line parameter:--valence:d/i d: default; i: ignore |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
#### 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. |
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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 CartridgeUse the jc_compare operator with checkSpHyb:Y/N.jcsearch command line toolUse the following command line parameter:--checkSpHyb:y/n |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |