On Tue, Sep 21, 2010 at 5:29 PM, James Davidson <[email protected]> wrote:
> Thanks for the VERY rapid response, Greg (it makes me think you have a
> pro-forma to answer SMARTS-related questions)!
:-)
>
> Greg wrote:
>> If you see anything different, I would certainly like to know
>> about it. In that case, please let me know which version of
>> the RDKit on which platform.
>
> I see the same (as you probably expected!). However, what I probably
> should have said to start with is that I am bringing my molecules in
> using an SD supplier. So:
>
> p = Chem.MolFromSmarts('[2#1,3#1]')
> suppl = Chem.SDMolSupplier(myfile)
> for mol in suppl:
> mol.HasSubstructMatch(p)
>
> Gives me a long list of 'False's. But your reply got me thinking, so
> doing the following actually gives the matching as expected:
>
>
> p = Chem.MolFromSmarts('[2#1,3#1]')
> suppl = Chem.SDMolSupplier(myfile)
> for mol in suppl:
> newMol = Chem.MolToSmiles(mol, True)
> newMol = Chem.MolFromSmiles(newMol)
> newMol.HasSubstructMatch(p)
>
>
> The SDF I am using was generated by RDKit via reaction enumeration. I'm
> confused!
hmm, here I don't understand what's going on. It *should* make no
difference if the molecule comes from an CTAB or a smiles. Would it be
possible to send a small version of the SDF showing the problem that
contains only non-proprietary structures?
Best regards,
-greg
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