Hi George,
I don't quite understand the problem with the canonical smiles although I'm
sure Greg will work it out. The molecule reads in fine from the original smiles.
>>> mol = Chem.MolFromSmiles("C1=CC=C2C(=C1)NC=S2")
>>> Chem.MolToSmiles(mol)
>>> 'c1[nH]c2ccccc2s1'
It would be less work (computationally) to write a try statement from the
original smiles and if that fails then handle it the way that you have shown.
Sorry I couldn't answer your exact question though, best of luck.
Best,
Nick
On 12 Mar 2012, at 16:58, George Papadatos wrote:
> Hello all,
>
> Could anyone please explain this:
>
> In [21]: Chem.CanonSmiles('C1=CC=C2C(=C1)NC=S2')
> Out[21]: 'c1[nH]c2ccccc2s1'
>
> In [22]: Chem.MolFromSmiles(Out[21])
> [16:47:14] Can't kekulize mol
>
> In other words, how is it possible that a valid RDKit SMILES output fails to
> be converted to molecule again?
> I'm sure this has to do with aromaticity and kekulization for benzothiazole
> but still....
>
>
> Many thanks in advance,
> George
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