On Sun, Jul 5, 2015 at 1:03 AM, Richard West <[email protected]> wrote:
>
> Secondly (and this may be a separate issue, and is of less urgency) it
> would be nice if I could represent these with distinct SMILES-like strings.
> I say “SMILES-like" because the strict Daylight SMILES spec may insist that
> they are all the same SMILES. But I would like to be able to represent
> those three forms of 2-Hydroxy-1-methylbenzene as Cc1ccccc1O, CC1C=CC=CC=1O
> and CC1=CC=CC=C1O respectively.
>
I don't have a clever solution for generating all of the Kekule forms on
hand, but once you do have them, it is no problem to generate Kekule SMILES:
In [6]: Chem.MolToSmiles(m)
Out[6]: 'Cc1ccccc1'
In [7]: Chem.Kekulize(m)
In [8]: Chem.MolToSmiles(m,kekuleSmiles=True)
Out[8]: 'CC1=CC=CC=C1'
Best,
-greg
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