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
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
