Hi, I would like to talk a bit about aromaticity and SDF interpretation in the CDK.
When I load a molecule, say a benzene, respecting the SDF Format regarding bond types (1 and 2 order), the CDK load this molecule as is, and set the aromatic flag to 1 when the aromaticity detection is performed. When I load the same molecule but with all bond types defined at 4 (aromatic), the CDK will directly set the aromatic flag to 1, but will define all bonds as SINGLE bonds. Now if I pass a benzene molecule with bond types defined at 4 through the CDK, and if I regenerate the SDF file without hydrogen, I will get... cyclohexane. If I add explicit hydrogen, I will get something that could be interpreted as benzene missing all double bonds, or cyclohexane missing one hydrogen for each carbon atom. Bellow is given a small snippet example. Maybe I'm doing something wrong, in which case I'm talking for nothing. If not, as such bond definition is not that uncommon (at least to my modest knowledge), I think this is an important issue. One possible solution would be to "dearomatize" the molecules, but the current CDK implementation is limited to benzene, pyridine & pyrrole. Just one question beside this discussion: why not putting the aromatic bond flag in the output in such cases? I also would have one suggestion on how to improve the CDK: defining a clear (customizable), documented standardization protocol which would include issues like aromatization/dearomatization, ionization, tautomerization, 2D/3D cleaning... The best example to my knowledge is the chemaxon's standardizer: http://chemaxon.com/jchem/doc/user/Standardizer.html Well, one suggestion among many others I guess :) Cheers! Vincent ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
