Yeah, it's clear that it would be useful to be able to have SMARTS in
tables, but don't forget that those fingerprints are used for substructure
screening. Using query molecules as the targets of a substructure search
(which is what you'd be doing in that case) is not always guaranteed to
produce the expected results.[1]
-greg
[1] That's my way of saying: be careful ;-)
On Fri, Mar 18, 2016 at 7:46 AM, Samo Turk <[email protected]> wrote:
> 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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>>
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