Hi Greg,
Thanks for quick reply!
I noticed that it works if it is constructed from SMILES, but the queries I
usually have are more complex and are constructed from SMARTS especially
because I also do some query adjustments (similar to what was discussed
here https://github.com/rdkit/rdkit/issues/567).
Cheers,
Samo
On Fri, Mar 18, 2016 at 2:25 PM, Greg Landrum <[email protected]>
wrote:
> 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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