On 21 February 2012 14:23, Martin Guetlein <[email protected]> wrote: > Hi Egon, > > thanks for your answer. Glad to hear that this is a known issue, > because it troubles me a lot. > >> 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. > > I there a way to do that automatically? > >> 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. > > Yes, it would be great to have some "compatibility mode" towards > OpenBabel. I am working on a piece of software that uses OpenBabel, > CDK and Jmol, and aromaticity causes a lot of problems. >
I would be glad if there is a "compatibility mode" across all chemists understanding of aromaticity, but it seems this is non-existent. Coming from engineering background, it was quite a shock that such base notion is ill-defined ;) From experience, Daylight aromaticity definition is quite generous, compared to the rest at our depiction page http://apps.ideaconsult.net:8080/ambit2/depict?search=O%3DC1C%3DCNC%28%3DO%29N1 Nina > Best regards, > Martin > > > > On Tue, Feb 21, 2012 at 12:09 PM, Egon Willighagen > <[email protected]> wrote: >> 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 > > > > -- > Dipl-Inf. Martin Gütlein > Phone: > +49 (0)761 203 7633 (office) > +49 (0)177 623 9499 (mobile) > Email: > [email protected] > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
