Toby,
On Mon, Jul 8, 2013 at 4:07 PM, Toby Wright <[email protected]> wrote:
>
> Disclaimer: I'm working with RDKit Q3 2012 for historical reasons, so it's
> not impossible this has already been fixed. Sorry if this is the case.
>
unfortunately it hasn't.
>
> I ran into a "Can't kekulize" bug writing a molecule that had previously
> been sanitized. On further investigation I discovered the following strange
> behaviour:
>
> >>> mol = Chem.MolFromSmiles("C1=CC=[B-](C)C=C1", sanitize=False)
> >>> Chem.SanitizeMol(mol)
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
> >>> Chem.SanitizeMol(mol)
> [14:42:18] Can't kekulize mol
>
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ValueError: Sanitization error: Can't kekulize mol
> >>> Chem.SanitizeMol(mol)
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>
> That is, the first and third (and subsequent) sanitizations work but the
> second does not. If I output the mol as a smiles string before the second
> sanitization I get C[b-]1ccccc1 but C[B-]1C=CC=CC1 after the second.
>
> Any ideas what's going on?
>
It's a bug. I'll try to get it fixed for the next release.
-greg
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