Hi, Greg, Thank you for being so open in your response, and I certainly agree with everything you just said. Here are my thoughts.
- Easily understandable explanation: - From the Daylight theory manual (and you've used similar language): *exocyclic double bonds do not break aromaticity.* - I'd alter this to *double bonds exocyclic to the ring in question do not break aromaticity*. (I.e., even if they are in other rings) - Beyond this, conventional electron counting explains everything in Francis's example and mine. - I've heard it asserted that introducing this modification would significantly slow down aromaticity perception. That is a real consideration which of course you can evaluate better than I. - This would be a major change and I would recommend being able to turn it on via a run-time flag before making it the default behavior. - This would allow user testing for performance and for the emergence of hidden gotchas at either the chemical or the computational level. I hope this is helpful, at least as a starting point for discussion. -P. On Tue, Oct 23, 2018 at 9:08 AM Greg Landrum <greg.land...@gmail.com> wrote: > > > On Tue, Oct 23, 2018 at 3:00 PM Peter S. Shenkin <shen...@gmail.com> > wrote: > >> >> It's difficult to fault RDKit for making the same mistake that everybody >> else blithely accepts; but it would be great, IMO, if it could do better >> than everyone else in this regard. >> > > Again, I have no argument whatsoever with this. But a half-assed fix is > worse than doing nothing. So in order for me to do something about it I > need: > "someone to explain how things should be changed to in a way that is > clear, unambiguous, and that would allow a human being looking at the > structure to relatively easily figure out whether or not a given ring is > aromatic." > > >
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