stereo search question

User b7aa615db3

04-04-2006 15:50:07

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?

ChemAxon a3d59b832c

04-04-2006 20:01:10

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