On Tue, 17 Jan 2017 16:52:36 +0000
Chris Arthur <chris.art...@bristol.ac.uk> wrote:

> ValueError: Sanitization error: Can't kekulize mol

In most case I have 'Can't kekulize mol' error for hetorocycle with hydrogen on 
nitrogen and smiles which have not explicite hydrogen on N.
Exempli gratia:

>>> Chem.MolFromSmiles('c1ccnc1')
[10:23:21] Can't kekulize mol 
>>> Chem.MolFromSmiles('c1cc[nH]c1')
<rdkit.Chem.rdchem.Mol object at 0x7f8d6a30a6e0>


> I can generate a smiles string from it (I had thought of doing a smiles to
> molecule conversion)

so if this is the issue, you can convert your Mol object to smiles add missing 
H and build Mol from this new smiles.

Regards,

RafaƂ

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