On Dec 7, 2007 5:47 PM, Nina Jeliazkova <[EMAIL PROTECTED]> wrote: > I don't feel restricting aromaticity perception only to max two fused rings > will be very useful. It will break lot of old code.
IMHO, not more than in the old solution was broken. PAHs are not easy material, and not every atom and/or bond is aromatic in the full system. Realize, that the old algorithm was only trying the implement the Hueckel rules, for which I have yet to see a statement on going beyond -1- ring. I would very much appreciate if you could write up some documentation on a general algorithm to detect aromaticity in PAHs indicating which atoms/bonds are aromatic and which are not. > If there is no workaround I would suggest again to retain both old and new > aromaticity detectors in > place. The old one was broken. Period. Really. The new one has more well-defined behavior. I am not against dedicated algorithms to find aromaticity, though. Oh, and if you can, you might answer my questions on experimental evidence of aromaticity: http://chem-bla-ics.blogspot.com/2007/11/evidence-of-aromaticity.html Another good read is: http://depth-first.com/articles/2007/11/28/smiles-and-aromaticity-broken Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
