Hi Michal,
On Mon, Jan 6, 2014 at 3:30 PM, Michal Krompiec
<michal.kromp...@gmail.com>wrote:
> Hello Greg,
> >>> Chem.MolToSmiles(Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O'))
> [14:25:55] Can't kekulize mol
>
>
The problem is, once again, in the pyrrole:
In [2]: Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O')
[15:38:53] Can't kekulize mol
If you add the "explicit" H, everything works:
In [3]: Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2[nH]ccc2)NC1=O')
Out[3]: <rdkit.Chem.rdchem.Mol at 0x108d22910>
This smiles was generated from ChemSketch. OpenBabel converts it to
> O=C1NC=CC1=C1C=C(c2[nH]ccc2)NC1=O which is correctly interpreted by
> RDKit (no problems with kekulization).
> But IMHO both representations are correct, am I wrong?
>
The SMILES c1cccn1 does not really contain sufficient information to figure
out what the user meant. The RDKit does not, in general, try to "guess"
intent, so it fails on that form. Daylight's depictor also does not process
that form of pyrrole.
It's possible to imagine adding a special case for pyrrole, but something
like Cc1nncc1 would still cause problems.
The fact that you're getting those SMILES at all is really a bug in
ChemSketch. It should be adding the H.
-greg
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