Is there any flag in RDkit to match both 'normal' aspirin and embedded
aromatic analogues?
The problem is that I can't modify user queries by hand in real time :)
On Wed, Sep 13, 2017 at 2:12 PM, Chris Earnshaw <cgearns...@gmail.com> wrote:
> 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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