>> I would definitely expect the SmilesParser to return full-fletched, >> fully connected molecules. > > Minor note: a SMILES does not require one single connected molecule.
True, I was referring deducing all bonds. > The correct bond orders is the problem (if not explicitely given in the > SMILES). Yes, I know this is the tough part. Though I still think it should be part of the SmilesParser. If SMILES was a format without connectivity given (like PDB) I would understand the need to do post-processing to get connectivity. But since SMILES defines the connectivity explicitly I would expect the SmilesParser to do this job as well. Andreas -- Andreas Schüller PhD student in the research group of Prof. Dr. Gisbert Schneider Johann Wolfgang Goethe University Beilstein-endowed Chair for Chemoinformatics Building B - 3rd floor Siesmayerstr. 70 60323 Frankfurt am Main Germany Tel.: +49 69 798 24879 Fax: +49 69 798 24880 http://www.modlab.de/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
