Hi Samo,
The problem is because the molecule was constructed from SMARTS. If you use
MolFromSmiles it should work.
Having said that: I believe that it should also be possible to do this for
a molecule contructed from SMARTS, in which case this would be a bug, but
I'm going to have to play with it a bit to be sure
-greg
On Fri, Mar 18, 2016 at 5:44 AM, Samo Turk <[email protected]> wrote:
>
> I have problems with substructure matching in pandas and it's caused by
> AvalonTools (L178 in current version of PandasTools). I'm not sure if this
> is a bug or I'm doing something wrong. Here is a version of the code with
> just Avalon part:
>
>
> from rdkit.Avalon import pyAvalonTools as pyAvalonTools
>
> x = Chem.MolFromSmarts('c1ccccc1')
>
> pyAvalonTools.GetAvalonFP(x,isQuery=True,bitFlags=pyAvalonTools.avalonSSSBits)
>
> ---------------------------------------------------------------------------ValueError
> Traceback (most recent call
> last)<ipython-input-119-37184767f515> in <module>() 1
> pyAvalonTools.GetAvalonFP(x,----> 2
> isQuery=True,bitFlags=pyAvalonTools.avalonSSSBits)ValueError: Sanitization
> error: Can't kekulize mol
>
>
> It works if I force Chem.PatternFingerprint as _fingerprinter
>
> Cheers,
> Samo
>
>
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