Craig, Thanks for bringing up your previous message, it's definitely relevant. Was that really in 2007?!
> I propose, for argument's sake, that we should be using a LSSR, "Largest Set > of Smallest Rings." It would go like this: A breadth-first search for rings, > which terminates when all ring atoms have been included in at least one ring, > but only after ALL cyclic paths of a given size have been enumerated. Since > the LSSR is computed specifically for aromaticity detection, it would stop at > some reasonable size, say 8-atom rings. There needs to be one small tweak. Henry Rzepa is an expert on computational chemistry of "weird" aromaticity. He suggested ~14-atom rings when I talked to him about this. >> Good grief, what a question! I think one can develop "generally agreed" >> rules for simple >> systems, but when there is no measure of agreement, as there is not for >> higher rings, it >> becomes VERY difficult. what, for example, is meant by "aromaticity". It >> could mean >> 1. conforms to a 4n+2 rule >> 2. But, as we have shown, this may in fact depend on the writhe of the ring >> 3. Depends on whether the bonds alternate or not. Well, it is thought >> [18] annulene >> DOES alternate, but its still aromatic! >> 3. Depends on the magnetic properties, ie diatropic, or paratropic ring >> currents? >> Well, higher annulenes have been shown to have BOTH (in concentric rings!!). >> >> As a rule of thumb, I would say search up to 14, and treat anything >> higher as a >> special case! > In extreme cases (fullerenes), this algorithm is still fast, O(nrings), > because you stop at three rings. Something like 760 steps per ring in a > fullerene, but it's still linear, not polynomial or exponential. And it's > only something like 760 steps if the thing turns out to be completely > non-aromatic. In a real fullerene, it would decide all the atoms were > aromatic in the first pass of the outer loop, and be finished. Considering this would replace our existing use of SSSR for aromaticity perception, this would be a huge win. I'd advocate that we still want to keep SSSR available for users, but if we can avoid it for aromaticity detection, our code will be significantly faster for most users. -Geoff ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
