bouille wrote: > Dear Greg > > How I can raise the following error ? > > 291475, COc1ccc(cc1)\C=C1\[S]=C(Nc2ccc(cc2)S(N)(=O)=O)NC1=O |t:11| > Traceback (most recent call last): > File "/home/bouille/DescriptorsCalcul/3mon3D.py", line 85, in <module> > sdf3D = Chem.MolToMolBlock(molH) > ValueError: Sanitization error: Can't kekulize mol > > Best Regards > > Christian de Bouillé > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > Dear Christian, I'm no expert regarding smiles strings, but the molecule has several rings (if I can read it correctly there are 3 separated rings). one of them is a five-membered ring containing a sulfur. Maybe RDKit chokes on the three bonds that the sulfur is connected with. Is that molecule really O.K. There should at least be a charge at the sulfur atom in the ring, otherwise we get an insane structure, don't we? Best regards, Markus
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