Hi,
I do not insist on using kekule forms. In fact, I said that using a
double bond between two aromatic atoms in a SMILES does not appear
problematic to me.
I was trying to say in the line you quoted that even if analysis of QM
results leads to a verdict of non-aromaticity, such a verdict should
not prevent us from creating canonical ("unique") SMILES using
aromatic atoms and bonds. The two actually have little to do with each
other.
( Start parenthetical remark:
Having said that, however, there are some situations where a SMILES is
traditionally created using aromatic types where that is unnecessary;
think furan and pyrrole. Aromatic types are unnecessary, because there
are no reasonable alternative kekule forms.
But even so, I am not at all arguing for elimination of aromatic types
from SMILES whenever feasible. It's fine with me if packages use
aromatic types for pyrrole and furan, and they for the most part do.
End parenthetical remark)
I've encountered a few situations where I would take issue with some
packages' use (or non-use) of aromatic types, and maybe (since we're
having fun with this topic) I'll post some of these at some point in a
different thread. But I don't feel this way about RDKit's
canonicalization of any of the systems we've been discussing in this
thread.
My point in this thread is the one stated in the Subject: line: there
are sometimes two equivalent SMILES that are canonicalized
differently. I'm happy to find that the prevailing view is in
agreement with my opinion that these specific cases are bugs. (Happy
only because that means they'll likely be fixed at some point!)
-P.
On Wed, Jun 17, 2015 at 1:34 PM, Dimitri Maziuk <[email protected]> wrote:
> On 06/17/2015 08:36 AM, Peter Shenkin wrote:
>> "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.
>
> Again, define "canonical". If you insist on using kekule form in a
> binary computer, you'll have to have 2 distinctly different canonical
> benzenes. That's just how a binary computer works.
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
