I think it's a great idea. Chris Morley had recommended similar concepts in
terms of implicit valence.
Yes, many of the stranger SMARTS patterns here are for "dodgy" SMILES that
should retain aromaticity. It's possible, perhaps to set some level of "if
it was initially flagged as an aromatic atom, be more lenient" rules in the
code.
I'd like to continue the concept of an annual release, so in the meantime,
I think experiments are welcome.
-Geoff
On Fri, Jan 27, 2017 at 3:03 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Hi there,
>
> Here's a heads-up on some work I've been prototyping.
>
> The aromatic atom typer currently uses SMARTS patterns in aromatic.txt
> to assign max/min values of pi electrons. A more efficient approach is
> to simultaneously match against all the SMARTS patterns rather than
> one at a time, and well, to avoid using SMARTS at all.
>
> I've attached a Python prototype that shows the general idea - see the
> function getMinMax (the calls to IsAromatic will have to be removed,
> but are unavoidable here; the "elif"s will become a switch statement;I
> need to think some more about explicit hydrogens). To my mind, the use
> of a direct lookup is as clear, if not clearer, than using SMARTS
> patterns.
>
> I note that the existing tests don't hit all of the patterns, and
> while I can find molecules in ChEMBL that hit almost all of the
> patterns, I'm not sure whether I can find ones where the corresponding
> atom turns out to be aromatic in the end. I have a feeling this is
> because the patterns were added in response to dodgy smiles (e.g.
> using n instead of [nH]) which were reported or found by Geoff.
>
> Regards,
> - Noel
>
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