Chemical terms specific search options

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

Chemical terms filter expression

Sets the chemical terms filter expression. For details of the expression syntax, see the Chemical Terms Evaluator Guide and its short reference . Use specific functions from the search context to refer to the query and the target molecules, the search hit array and its elements.

WARNING: You may need to purchase seperate licenses to apply this option depending on the Chemical Terms used (logp, logd, ...)

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setChemTermsFilter
( <chemical terms expression> ); // ... MolSearch searcher = new MolSearch(); searcher.setSearchOptions(searchOptions);
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setChemTermsFilter( <chemical terms expression> );
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
JChem Oracle Cartridge
Use the jc_compare operator ctFilter :chemical-terms-expression
 
Example: The following SQL query returns the number of the structures that contain at least one benzene ring and have logP values greater than 9:
 
SELECT count(*) FROM nci_10m WHERE jc_compare(structure, 'c1ccccc1', 'sep=! t:s!ctFilter:logp()>9') = 1;
jcsearch command line tool
Use the following command line parameter:
 
-e "expression" / file name
or
--expression "expression" / file name

Ignore chemical terms evaluation error

Specifies whether to ignore exceptions during evaluation of expressions. Those molecules that return exception during evaluation will be left out from hit list. Syntactical errors of CT expression cannot be ignored!

MolSearch API
MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setIgnoreCTExceptions( true / false );
// ...
MolSearch searcher = new MolSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is false.
JChemSearch API
JChemSearchOptions searchOptions = new JChemSearchOptions(SearchConstants.SUBSTRUCTURE);
searchOptions.setIgnoreCTExceptions( true / false );
// ...
JChemSearch searcher = new JChemSearch();
searcher.setSearchOptions(searchOptions);
 
Default value is false.
JChem Oracle Cartridge
Use the jc_compare operator ignoreCTExceptions:y/n
 
Default value is n.
jcsearch command line tool
Use the following command line parameter:
 
--ignoreCTExceptions:y/n
 
Default value is n.