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From: Nina J. <ni...@ac...> - 2009-03-16 16:29:49
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Dear All, My name is Nina Jeliazkova and I’m the lead developer of the Toxtree application (http://toxtree.sourceforge.net), which relies on Open Babel for certain format conversions. We have received user feedback about problems with the following smiles: c12-c3c(cc(N)cc3)Cc1cccc2 We have traced down the problem to the following info messages, generated by Open Babel during smi->sdf and smi->smi conversions: babel ---errorlevel 2 -h -ismi c12-c3c(cc(N)cc3)Cc1cccc2.smi -osmi c12-c3c(cc(N)cc3)Cc1 cccc2-ob.smi ============================== *** Open Babel Information in OpenBabel::OBMol::NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule ============================== *** Open Babel Information in OpenBabel::OBMol::start_kekulize Kekulize Error for molecule 1 molecule converted 2 info messages 44 audit log messages The obtained output is clearly wrong: C12=C3C(=CC(=CC3)N)CC1C=CC=C2 We have also tried Daylight depict function, available at: http://www.daylight.com/daycgi/depict/ The later parses and depicts c12-c3c(cc(N)cc3)Cc1cccc2 correctly. We are well aware that kekule/aromatic standardization efforts are far from satisfactory so far, however we would like to have your interpretation of this problem. In particular, is Open Babel behaving as expected in this particular case? Kind regards, Nina |