Hi all,
I was playing around with the RGroup decomposition code and must say that I am
pretty impressed by it. The fact that one can directly work with a MDL R-group
file and that the output is a pandasDataFrame makes analysis really slick -
well done !
However, one thing that irritates me is the fact that seemingly when I have
R-groups defined in my core and enforce matching only at R-groups then
molecules having hydrogen atoms in that position are ignored in the "Add" step.
I would expect those to be included as long as the molecules don't have
additional heavy atoms in positions that are not defined as R-groups in the
core.
______________ snip ____________________
from rdkit import Chem
from rdkit.Chem.rdRGroupDecomposition import RGroupDecomposition,
RGroupDecompositionParameters
smis = ['Cc1ccnc(O)c1', 'Cc1cc(Cl)ccn1', 'Nc1ccccn1', 'Nc1ccc(Br)cn1',
'c1ccncc1']
mols = [Chem.MolFromSmiles(smi) for smi in smis]
params = RGroupDecompositionParameters()
params.onlyMatchAtRGroups = True
# just atom number the rgroups
core1 = Chem.MolFromSmiles('n1ccc([*:2])cc([*:1])1')
rg1 = RGroupDecomposition(core1, params)
failMols = []
for m in mols:
res = rg1.Add(m)
if res < 0:
failMols.append(m)
rg1.Process()
print("FailedMols: %s"%" ".join([Chem.MolToSmiles(m) for m in failMols]))
____________ end snip ________________
the output shows that molecules 3-5 are not included at the "Add" step
>> FailedMols: Nc1ccccn1 Nc1ccc(Br)cn1 c1ccncc1
For molecules 4 (the 5-bromo substituted aminopyridine) I agree, however I
don't understand how I can make sure mols 3 and 5 are also included ... is
there a magic parameter that I can set?
Cheers
Nik
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