To make my point clear finally :-) I would expect the SmilesParser to deduce bond orders, even if they were not explicitly given.
Andreas Egon Willighagen wrote: > On 9/25/07, Andreas Schüller <[EMAIL PROTECTED]> wrote: >> 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. > > Sure. The connectivity is really no problem; it is explicitely given, > and is and will ever be read by the SMILES parser. This never was a > problem. > > Bond orders are different. Even for PDB files deducing unknown bond > orders is easier (using some simple bond length heuristics, as > implemented in the RebondTool). A benzene ring (c1ccccc1) is no > problem either... but that are more complex examples, for which > deducing bond orders (not connectivity!) is a problem. > > Egon > -- 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
