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 <[email protected]> wrote:
>
>
> On Tue, Oct 23, 2018 at 3:00 PM Peter S. Shenkin <[email protected]>
> 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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