Hi Pascal,
It works for me:
>>> mol = pybel.readstring("smi", "c1cc2cccnc2c(c1)SC[C@@H]1CCOCO1")
>>> acetal =
>>> pybel.Smarts("([OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])])")
>>> acetal.findall(mol)
[(17, 16, 18, 19, 13)]
>>>
- Noel
On 12 October 2010 07:53, Pascal Muller <[email protected]> wrote:
> Hi,
>
>> Can you provide a SMILES string for an example molecule that works
>> with obgrep but not Pybel?
>
> Sure, e.g.
> CC1(COC(OC1)c1ccccc1)C(=O)NCc1ccco1 ZINC00034365
> c1cc2cccnc2c(c1)SC[C@@H]1CCOCO1 ZINC00032596
>
> Regards,
> Pascal
>
>
>>> I would like to filter e.g. acetal and aminal, with pybel and smarts.
>>>
>>> I use the following syntax:
>>>
>>> acetal =
>>> pybel.Smarts("([OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])])")
>>>
>>> but len(acetal.findall(mol)) is equal to zero - acetal present or not.
>>>
>>> But obgrep with the same smarts on the same smiles file retrieve the
>>> corresponding molecules.
>>>
>>> Any suggestions for getting this working?
>>>
>>> Other smarts like
>>> pybel.Smarts("[#6^3]Cl")
>>> works well (the ^3 / sp3 feature is great :)
>>>
>>> Thanks!
>>> Regards,
>>> Pascal
>
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