On 7/2/10 4:44 AM, Tim Vandermeersch wrote: > Hi, > > I have put the "old" aromaticity algorithm back since unit tests were > failing. I tried to debug the problem but didn't get far. When Craig > has time to look at this, I can merge this again. > > Although electron counting isn't the problem with the failing unit > test, Craig has a point. There should be no ambiguous electron > contributions in the aromaticity model. It doesn't seem to be > difficult to fix this but some decision have to be made. A possible > strategy would be: > > * Use Hückel 4n + 2 rule
It seems you have to modify Hueckle's rule a bit -- you have to subtract 2 electrons for a ring-of-rings (4n+2 becomes just 4n), like this: http://www.emolecules.com/image?smiles=c1cc2ccc3ccc4ccc5ccc1c1c5c4c3c21&coordinates=2.7079,-1.72,4.44,-1.72,5.306,-2.22,6.17\21,-2.72,6.1721,-3.72,5.306,-4.22,5.306,-5.22,4.44,-5.72,3.574,-5.22,2.7079,-5.72,1.8419,-5.22,1.8419,-4.22,0.9759,-3.7\2,0.9759,-2.72,1.8419,-2.22,2.7079,-2.72,2.7079,-3.72,3.574,-4.22,4.44,-3.72,4.44,-2.72 It seems you have to subtract more (4n, 4n-2, 4n-4 etc.) for larger cage structures like fullerenes, but I haven't figured out the rule for that yet. It's something like: "If the SSSR has N rings, but you can find K rings of the SSSR that span all the atoms and bonds, then subtract 2*(N-K) electrons from Hueckle's rule." But that's a very roundabout way of expressing it. I suspect I'm not the first to figure this out ... does anyone has a clear, algorithmic way to express this extended Hueckel's rule? Craig ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
