Hi,
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.
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?
Yours,
Toby Wright
--
InhibOx
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