Re: [Rdkit-discuss] SMILES: Why are rings consisting of wildcards assumed to be aromatic?

[Peter S. <sh...@gm...>]

On Mon, Jun 15, 2015 at 9:54 AM, Greg Landrum <gre...@gm...>
wrote:
>
> On Thu, Jun 11, 2015 at 5:54 PM, Peter Shenkin <sh...@gm...> wrote:
>
>> If I canonicalize *1**1 in RDKit, I get  [*]1:[*]:[*]:1.
>>
>> I expected [*]1[*][*]1.
>>
> ...
>
> This is certainly a bug and I've put it on the list of stuff to fix:
> https://github.com/rdkit/rdkit/issues/518
>
>
Thanks much, Greg. That is very helpful.

Pursuing another remark you made, RDKit canonicalizes C1=C*C=C1
as [*]1cccc1. This may also be unwarranted, because the wildcard could be
another C, in which case the structure would not be aromatic.

-P.