This is reviving a long-dead thread because I just marked the associated
issue as "won't fix" and some of you might be interested in the reasons.
Here's the bug: https://github.com/rdkit/rdkit/issues/523
The comment explaining my thinking is here:
https://github.com/rdkit/rdkit/issues/523#issuecomment-203247157
If possible, please continue the discussion as part of the github issue. If
you don't have a github account and aren't willing to get one, we can
continue here.
Because discussions about aromaticity have a tendency to get heated and
off-topic very quickly, please do read the explanation of the RDKit's
aromaticity model here: http://rdkit.org/docs/RDKit_Book.html#aromaticity
before commenting. If you have an argument with the aromaticity model,
please start a separate thread for it.
Though a change to the model to treat anti-aromatic systems as aromatic
would resolve it, this particular issue is *not* about how aromaticity is
modeled.
Best,
-greg
On Wed, Jun 17, 2015 at 8:22 AM, Peter Shenkin <[email protected]> wrote:
> Hi, Greg,
>
> Within the SMILES framework, it seems to me that if you allow the atoms to
> be aromatic, then these are two Kekule structures of the same aromatic
> system, and however you do the canonicalization, they ought to canonicalize
> to the same structure, which the two examples did not do. I don't think you
> addressed this.
>
> I think now that there is no issue with having a double bond between two
> aromatic atoms beyond our preconceptions. If that is a problem, you could
> Kekulize it per your first picture, (though perhaps that is inconvenient in
> the context of the implementation).
>
> I actually didn't realize why aromaticity (particularly the double bond)
> made sense when I originally wrote, so the above is with the benefit of
> hindsight, and your comments.
>
> I think the molecule is entertaining in several ways. In the cubane
> geometry, the molecule cannot be conventionally aromatic. Might it actually
> be antiaromatic? Could there be two forms?
>
> Dunno....
> -P.
>
>
> On Wed, Jun 17, 2015 at 1:25 AM, Greg Landrum <[email protected]>
> wrote:
>>
>>
>> The problematic part of your two molecules can be reduced to:
>> [image: Inline image 3]
>> and
>> [image: Inline image 4]
>> That second one shows the kekulized form that the RDKit ends up using.
>>
>> These produce the following canonical SMILES:
>>
>> In [31]: Chem.CanonSmiles('C1=CC2=CC=C12')
>> Out[31]: 'c1cc2ccc1-2'
>>
>> In [32]: Chem.CanonSmiles('C1=CC2=C1C=C2')
>> Out[32]: 'c1cc2ccc1=2'
>>
>>
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