stereo search question

Based on the stereo bond information on the JChem Query Guide (http://www.chemaxon.com/jchem/doc/user/Query.html#stereobond) I would expect the following to find a match:





jcsearch -t:e -q "C\C(C([O-])=O)=C(\Cl)C(=O)CC([O-])=O" -s "CC(C([O-])=O)=C(Cl)C(=O)CC([O-])=O





jcsearch 3.1.5 and TEST_2006_03_16 does not return a match. Am I misunderstanding the Guide?

Hi Dave,





Please note that in case of a smarts/smiles query, there is no such thing as "marked" double bond (which is depicted as a square over the double bond). (The file formats miss this feature.) So, for these file formats all specified double bond stereo configurations are checked by default.





(See this link about how the query file format affects searching: http://www.chemaxon.com/jchem/doc/user/Query.html#DiffDBS)





To ignore all double bond stereo info, I recommend the --doubleBondStereo:N option:

Code:

$ jcsearch --doubleBondStereo:N -t:e -q "C\C(C([O-])=O)=C(\Cl)C(=O)CC([O-])=O" -s "CC(C([O-])=O)=C(Cl)C(=O)CC([O-])=O" CC(C([O-])=O)=C(Cl)C(=O)CC([O-])=O

Best regards,


Szabolcs