On Tue, Jul 9, 2013 at 5:40 AM, Greg Landrum <[email protected]> wrote:
>
>
>>
>> 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.
>
>
I just checked in a fix.
-greg
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