Inconsistent aromatic behaviour

Hi


select jc_equals('c1ccccc1', 'C1=C-C=C-C=C1') from dual; --yes they are equal





select jc_equals('CC1=C(CCCl)C(=O)N2C=CSC2=N1','Cc1nc2sccn2c(=O)c1CCCl') from dual; --no they are not





why is this? In reality, of course, the search is being performed on a jchem indexed column in the database, and actually I am using jc_compare with t:e.





JChem version: 3.1.1


JChem Streams version: 3.1.1





Thanks


Mark (Evotec)

Dear Mark,





The given Kekule structure is not aromatic according to Chemaxon aromatization(basic) -- this is the default in 3.1.1, but it is with Daylight aromatization(general). If you prefer the latter, please make sure to use a custom standardization on the table. (E.g. a standardization rule of "aromatize:d" should suffice.)





From the next major release (3.2), the default aromatization will change to general.





Best regards,





Szabolcs

Mark,





In the context of JChem Cartridge, having a custom standardization on structure tables means using the "std_config" jc_idxtype index parameter ( http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#index ).





For searches without a table (FROM DUAL et al.) and without jc_idxtype index information, you can use the jc_set_default_property operator ( http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#defaultproperties ).





Peter