Hi Mark, On Thu, Aug 12, 2010 at 6:07 PM, Mark Rijnbeek <ma...@ebi.ac.uk> wrote: > I was wondering: if the structure has explicit aromaticity bonds, would > it not be better to preserve this in the container? Rather than > overruling it with the CDK's aromaticity detection.
AFAIK the SMILES specification dictates that the parser detects the aromaticity... The OpenSMILES specs have this to say about it: "In an aromatic system, all of the aromatic atoms must be sp2 hybridized, and the number of Pi electrons must meet Hückel's 4N+2 criterion. When parsing a SMILES, a parser must note the aromatic designation of each atom on input, then when the parsing is complete, the SMILES software must verify that electrons can be assigned without violating the valence rules, consistent with the sp2 markings, the specified or implied hydrogens, external bonds, and charges on the atoms." Really, I have been having discussions over this since the start of the CDK... please have a look in the archives for the full discussions... What about making an option: "Don't verify aromaticity, and take whatever is encoded in the SMILES" ? It would not reflect the SMILES specification, but everyone seems a bit agnostics about the specs and use it in whatever way they think is suitable... I'm done discussing SMILES... Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
