Hi Grégori,
On Mon, Oct 29, 2012 at 10:05 AM, Gerebtzoff, Gregori
wrote:
>
> Is there a clean way to capture the warnings generated by RDKit, for
> instance “Warning: ring stereochemistry detected. The output SMILES is not
> canonical”?
>
> I tried several approaches (the warnings python module, by redirecting the
> stderr with os.devnull, or try/except) but none of them allowed me to
> capture these warnings.
unfortunately there's no way to capture errors or warnings to a file.
You can disable all the warning messages:
In [4]: from rdkit import RDLogger
In [5]: lg = RDLogger.logger()
In [6]: Chem.CanonSmiles('C[C@H]1CC[C@H](C)CC1')
[06:01:43] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
[06:01:43] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
Out[6]: 'C[C@@H]1CC[C@@H](C)CC1'
In [7]: lg.setLevel(RDLogger.ERROR)
In [8]: Chem.CanonSmiles('C[C@H]1CC[C@H](C)CC1')
Out[8]: 'C[C@@H]1CC[C@@H](C)CC1'
In [9]: lg.setLevel(RDLogger.WARNING)
In [10]: Chem.CanonSmiles('C[C@H]1CC[C@H](C)CC1')
[06:02:04] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
[06:02:04] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
Out[10]: 'C[C@@H]1CC[C@@H](C)CC1'
or you can send warning and error messages to a file by redirecting stderr:
~ > python -c "from rdkit import
Chem;Chem.CanonSmiles('C[C@H]1CC[C@H](C)CC1')" 2> err.txt
~ > cat err.txt
[06:03:37] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
[06:03:37] Warning: ring stereochemistry detected. The output SMILES
is not canonical.
But this only helps outside of the RDKit.
I've avoided spending any real time on this because getting logging
right is tricky and there is, theoretically, a boost logging library
coming. Of course, it's been theoretically coming for a couple of
years now, so maybe it's time to give up.
-greg
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