On 26/04/2021 23:35, Greg Landrum wrote:
Hi Francois,
The implementation which is there does, I believe, the right thing.
However... first you need to find the Murcko Scaffold, then you can
convert that scaffold to the generic form:
In [5]: m = Chem.MolFromSmiles('CCc1ccc(O)cc1C(=O)C1CC1')
In [6]: scaff = MurckoScaffold.GetScaffoldForMol(m)
In [7]: Chem.MolToSmiles(scaff)
Out[7]: 'O=C(c1ccccc1)C1CC1'
In [8]: framework = MurckoScaffold.MakeScaffoldGeneric(scaff)
In [9]: print(Chem.MolToSmiles(framework))
CC(C1CCCCC1)C1CC1
Ok, maybe this two steps process is a little bit better, but still
not exactly what I would expect in some cases.
I'll say if I program something which I prefer.
Best,
-greg
On Mon, Apr 26, 2021 at 11:15 AM Francois Berenger <mli...@ligand.eu>
wrote:
Hello,
I am trying MurckoScaffold.MakeScaffoldGeneric(mol),
but this keeps the side chains.
While my understanding of BM scaffolds is that only rings
and ring linkers should be kept.
The fact that the rdkit implementation keeps the
side chains makes Murcko scaffolds a much less powerful filter
to enforce molecular diversity.
And I don't even see any option to force the standard/vanilla
behavior.
Or, am I missing something?
Regards,
F.
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
