I should mention on that note, that a collaboration with Carnegie Mellon
students produced a parallel implementation of Kekulization using the
Eigen3 matrix library. They also wrote a CUDA implementation that was
modestly faster.
It hasn't been ported back to Open Babel yet, but I'll leave the basic code
(MIT license) here:
https://github.com/NarainKrishnamurthy/chemposer
Anyone interested should let me know..
Cheers,
-Geoff
On Fri, Jan 27, 2017 at 5:13 PM, Geoffrey Hutchison <
ge...@geoffhutchison.net> wrote:
> 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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