On 27/04/2021 10:12, Francois Berenger wrote:
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.
Hello,
I end up with this:
---
def find_terminal_atoms(mol):
res = []
for a in mol.GetAtoms():
if len(a.GetBonds()) == 1:
res.append(a)
return res
# Bemis, G. W., & Murcko, M. A. (1996).
# "The properties of known drugs. 1. Molecular frameworks."
# Journal of medicinal chemistry, 39(15), 2887-2893.
def BemisMurckoFramework(mol):
# keep only Heavy Atoms (HA)
only_HA = rdkit.Chem.rdmolops.RemoveHs(mol)
# switch all HA to Carbon
rw_mol = Chem.RWMol(only_HA)
for i in range(rw_mol.GetNumAtoms()):
rw_mol.ReplaceAtom(i, Chem.Atom(6))
# switch all non single bonds to single
non_single_bonds = []
for b in rw_mol.GetBonds():
if b.GetBondType() != Chem.BondType.SINGLE:
non_single_bonds.append(b)
for b in non_single_bonds:
j = b.GetBeginAtomIdx()
k = b.GetEndAtomIdx()
rw_mol.RemoveBond(j, k)
rw_mol.AddBond(j, k, Chem.BondType.SINGLE)
# as long as there are terminal atoms, remove them
terminal_atoms = find_terminal_atoms(rw_mol)
while terminal_atoms != []:
for a in terminal_atoms:
for b in a.GetBonds():
rw_mol.RemoveBond(b.GetBeginAtomIdx(),
b.GetEndAtomIdx())
rw_mol.RemoveAtom(a.GetIdx())
terminal_atoms = find_terminal_atoms(rw_mol)
return rw_mol.GetMol()
---
I don't claim this is very efficient Python code. I am not very good at
snake charming.
Regards,
F.
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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