Hi

The problem is due to RDkit perceiving the embedded pyranone in
CHEMBL1999443 as an aromatic system, which is probably correct. However, in
the structure of aspirin the carboxyl carbon and singly bonded oxygen are
non-aromatic, so if you just use the SMILES of aspirin as a query it won't
match CHEMBL1999443

You'll need to use a slightly more generic aspirin-like query to allow the
possibility of matching both 'normal' aspirin and embedded aromatic
analogues. CC(=O)Oc1ccccc1[#6](=O)[#8] should work OK.

Regards,
Chris

On 13 September 2017 at 13:40, Michał Nowotka <mmm...@gmail.com> wrote:

> Hi,
>
> This problem is probably due to my lack of chemistry knowledge but
> plese have a look:
>
> If I do a substructure search in ChEMBL using aspirin (CHEMBL25) as a
> query (ChEMBL API uses the Symix catridge):
>
>     from chembl_webresource_client.new_client import new_client
>     res = new_client.substructure.filter(chembl_id='CHEMBL25')
>
> One of them will be CHEMBL1999443:
>
>     'CHEMBL1999443' in (r['molecule_chembl_id'] for r in res)
>     >>> True
>
> Now I take the molfile:
>
>     new_client.molecule.set_format('mol')
>     mol = new_client.molecule.get('CHEMBL1999443')
>
> and load it with aspirin into rdkit:
>
>     from rdkit import Chem
>     m = Chem.MolFromMolBlock(mol)
>     pattern = Chem.MolFromMolBlock(new_client.molecule.get('CHEMBL25'))
>
> If I check if it has an aspirin as a substructure using rdkit, I'm
> getting false...
>
>     m.HasSubstructMatch(pattern)
>     >>> False
>
> Looking at this blog post:
> https://github.com/rdkit/rdkit-tutorials/blob/master/notebooks/002_SMARTS_
> SubstructureMatching.ipynb
> I tried to initialize rings and retry:
>
>      Chem.GetSymmSSSR(m)
>      m.HasSubstructMatch(pattern)
>      >>>False
>
>     Chem.GetSymmSSSR(pattern)
>     m.HasSubstructMatch(pattern)
>     >>>False
>
> But as you can see without any luck. Is there anything else I can do
> to get the match anyway?
> Without having a match I can't aligh and higlight asprin substructure
> in CHEMBL1999443 image using GenerateDepictionMatching2DStructure and
> DrawMolecule functions.
>
> Kind regards,
>
> Michał Nowotka
>
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