Egon Willighagen wrote: > On 9/29/07, Rajarshi Guha <[EMAIL PROTECTED]> wrote: >> On Sep 29, 2007, at 9:49 AM, Christoph Steinbeck wrote: >>> Andreas Schüller wrote: >>>> To make my point clear finally :-) >>>> >>>> I would expect the SmilesParser to deduce bond orders, even if >>>> they were not explicitly given. >>> CDK's approach to this should always be that of Lego(TM): Provide >>> building blocks and not monolithic solutions. >>> >>> The SMILESParser should parse what is in the SMILES and not more. >>> If the chemoinformatician then desires to do more, he or she will >>> apply a BondOrderResolver or an AromaticityDetector or whatever. >>> >>> To be explicit: We shall not try to deduce bond orders which are not >>> explicitly given from within SMILESParser, but CDK will need to >>> provide >>> additional building blocks for this, so one can do it if one needs to. >>> >>> This is a toolkit library and should be of greatest modularity >>> possible. >> But I think there should be a class built-in that does put all the >> peices together. >> I'm pretty sure that this will trip many up - when a SMILES is >> parsed, it is intuitive to expect a full fledged molecule > > Mmm... What about type 4 bonds in MDL files then? Should we do the > bond order deduction there too then? > > Why not simple WYSIWYG? -> You see no double bonds (SMILES, MDL), but > marks of sp2 (SMILES) or aromaticity (MDL bond type 4), so you get no > double bonds but markers of sp2 or aromaticity.
I agree. What you get *is* a fully fledged molecule. It is connected, has all the element symbols and the bond orders (e.g. "aromatic") or attributes that were in the SMILES. After all, having alternating patterns of double and single bonds where there should be "aromatic" is not exactly correct, right :-) Cheers, Chris -- PD Dr. Christoph Steinbeck Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ------------------------------------------------------------------------- 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
