Hi Martin, On Tue, Feb 21, 2012 at 11:39 AM, Martin Guetlein <[email protected]> wrote: > I found another example ( O=C1C=CNC(=O)N1 ) that is not aromatic > according to CDK, but according to daylight > (http://www.daylight.com/daycgi/depict?4f3d4331433d434e43283d4f294e31) > and OpenBabel. Is this a bug?
No, it is not a bug. It is a difference in the algorithmic definition of aromaticity: http://apps.ideaconsult.net:8080/ambit2/depict?search=O=C1C=CNC(=O)N1 And, incidentally, exactly what I talked about in my talk for NBIC last Thursday [0]. The CDK algorithm for aromaticity defines rings with double bonds pointing out of the ring as non-aromatic; for this compound to be aromatic, it would require a charge separation on the double bonds, which you can reflect in the chemical graph. Doing that, should make the compound aromatic. Compare the above depictions with these: http://apps.ideaconsult.net:8080/ambit2/depict?search=%5BO-%5D%5BC%2B%5D1C%3DCN%5BC%2B%5D%28%5BO-%5D%29N1 The fact that the CDK did not mark that representation as aromatic, would be a bug (and it should be filed). Nina, if you are reading this, can I request a similar depiction service, visualizing the atom types labels for each atom? BTW, the CDK is very open to alternative algorithmic definitions of 'aromaticity'. We currently only have one 'standard' implemented, and for long I have wanted to implement other standards too. Not that I am aware of any algorithm being standardized on, or even just published. Aromaticity is one of the most misunderstood concepts in cheminformatics :) (Not claiming I understand all aspects of it...) Egon 0.http://chem-bla-ics.blogspot.com/2012/02/chemical-interoperability.html -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
