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

Reply via email to