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
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.
>
>
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