"We could consider some quantum-mechanical calculations "
Yes! for the question of "the true nature" of the molecule. But that not
need not affect the way canonicalization is done.
These are two different forms of entertainment....
-P.
On Wed, Jun 17, 2015 at 3:24 AM, Markus Sitzmann <markus.sitzm...@gmail.com>
wrote:
> We could consider some quantum-mechanical calculations ... well, I always
> hated this discussion when I heard for my web service with millions of
> structures, I should consider quantum-mechanical calculations as part of
> the structure normalization/canonicalization ;-)
>
> On Wed, Jun 17, 2015 at 8:22 AM, Peter Shenkin <shen...@gmail.com> 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 <greg.land...@gmail.com>
>> 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'
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
