Hi Zhenting,
This work fine for me with both the 2020.03 release:
In [6]: print(rdkit.__version__)
2020.03.1
In [7]: from rdkit import Chem
In [8]: p =
Chem.MolFromSmarts('c1:c:c(:c:c:c:1-[#8]-[#6&X4])-[#7;$([#7&!H0]-[#6&X4]),$([#7](-[#6&X4])-[#6&X4])]')
In [9]: m = Chem.MolFromSmiles('N2C(C1(CCCC1)Cc3c2cc(c(c3)OC)OC)CC=C')
In [10]: m.HasSubstructMatch(p)
Out[10]: True
and the 2019.09 release:
In [1]: import rdkit
In [2]: print(rdkit.__version__)
2019.09.3
In [3]: from rdkit import Chem
In [4]: m = Chem.MolFromSmiles('N2C(C1(CCCC1)Cc3c2cc(c(c3)OC)OC)CC=C')
In [5]: p =
Chem.MolFromSmarts('c1:c:c(:c:c:c:1-[#8]-[#6&X4])-[#7;$([#7&!H0]-[#6&X4]),$([#7](-[#6&X4])-[#6&X4])]')
In [6]: m.HasSubstructMatch(p)
Out[6]: True
Can you please share a code snippet that shows the problem?
-greg
On Thu, Apr 23, 2020 at 7:26 PM Zhenting Gao <[email protected]> wrote:
> Hi there,
>
> I'm trying to filter a compound list by PAINS filter.
> With SMARTS query
>
> 'c1:c:c(:c:c:c:1-[#8]-[#6&X4])-[#7;$([#7&!H0]-[#6&X4]),$([#7](-[#6&X4])-[#6&X4])]'
>
> KNIME can identify the following SMILES as a match
> 'N2C(C1(CCCC1)Cc3c2cc(c(c3)OC)OC)CC=C'
>
> But I can't identify the same SMILES with RDkit 2019.9.3.
> I guess the difference is aromaticity mismatch. Could you help?
>
> Best regards
> Zhenting
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
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