I would definitely expect the SmilesParser to return full-fletched, fully connected molecules.
Actually, I don't find it intuitive to need a post-processor for the SmilesParser. So the SMILES parser should: 1. Parse the SMILES into a connectivity table 2. Resolve the connectivity table and deduce bond orders 3. Return a fully connected molecules with correct bond orders It doesn't need to 1. Detect aromaticity, unless explicitly given in the SMILES 2. Add hydrogens unless explicitly given in the SMILES I was hoping on fixing the remaining SmilesParser bugs with your new, improved atom typing. Cheers, Andreas Egon Willighagen wrote: > (OK, KMail + Gmail is not a friendly combination... the slighest > mistype results in an undesired submit :( ) > > On 9/25/07, Egon Willighagen <[EMAIL PROTECTED]> wrote: >> in this email I would like to bring forward a request for comments >> (RFC) about the SMILES parser. >> >> One thing that CDK 1.0 has clarified is the difficulties it has with >> deducing bond orders, for which it was tried to write a >> one-size-fits-all algorithm using available atom type lists. This >> failed. One workarou > > ... One workaround is the DeduceBondOrderTool which takes a rule based > approach, which will never provide a full coverage, but at least > succeeds to do the most common things right. > > Getting to the SMILES parser, I would like to request comments on what > functionality is to be expected from a SMILES parser. To make the > SMILES parser in the CDK back into a consistent working state again, I > would like to suggest it will no longer try to resolve bond orders and > leave that to the user as post-processing. This will fix all standing > open bugs in the CDK SmilesParser, which are all related to failing > bond order resolution. > > The SMILES parser should: > 1. parse the SMILES into a connectivity table > 2. mark atoms which lower case symbols for steps 2 and 3 > 3. try to resolve bond orders for atom groups which do not include ring atoms > 4. try to deduce bond orders for atom groups which include ring atoms only for > very well defined groups using a rule-based approach > 5. detect aromaticity for single, isolated ring systems only > > Not really too different from what is happening right now, but cleaner > and better defined. > > Is the above all we should expect the SMILES parser to do? > > 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
