Oh, good question. That may be a bug, I suspect some testing is in order.
Geoff
On Sat, Jan 24, 2015 at 5:57 AM Eva Lacy <e...@lacy.ie> wrote:
> Thanks Geoffrey,
>
> So the bit I'm confused about and forgive me cause I'm not a chemist, is
> given that it uses the capital N in N^2 rather than lowercase or the
> generic form this means it's explicitly aliphatic, but pyrrole is aromatic,
> surely it shouldn't match even if it is sp2?
>
> Eva
>
> On 23 January 2015 at 18:19, Geoffrey Hutchison <geoff.hutchi...@gmail.com
> > wrote:
>
>> > I'm having some difficulty understanding how Pyrrole matches with the
>> SMARTS string N^2 given that it's aromatic.
>>
>> The ^ pattern is an extension to SMARTS. It indicates matching a
>> particular hybridization (i.e., sp2 here). Certainly pyrrole has an sp2
>> nitrogen.
>>
>> What happens is that hybridization must be assigned, so a whole new set
>> of SMARTS are run to assign hybridizations. There have been some efforts to
>> write implicit valence rules without SMARTS.
>>
>> -Geoff
>
>
>
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