Hi,
I’m using the new R group decomposition code in version 2021.03.1 and I’m
receiving some strange cores when I have R groups within rings. Here is my
example code:
from rdkit import Chem
from rdkit.Chem import rdRGroupDecomposition as rdRGD
core = "O=C(Cc1cccc(Cl)c1)Nc1cncc2c[*:1]:[*:2]cc12”
compounds = ["c1cc(cc(c1)Cl)CC(=O)Nc2cncc3c2ccnc3”,
"c1cc(c(cc1CC(=O)Nc2cncc3c2ccnc3)Cl)Cl”,
"c1cc(cc(c1)Cl)CC(=O)Nc2cncc3c2cncc3”]
core_smarts = Chem.MolFromSmarts(core)
compound_mols = [Chem.MolFromSmiles(x) for x in compounds]
R_opts = rdRGD.RGroupDecompositionParameters()
R_opts.allowNonTerminalRGroups = True
R_opts.removeAllHydrogenRGroupsAndLabels = False
Rgroups, remainder = rdRGD.RGroupDecompose(core_smarts, compound_mols,
asSmiles=True, asRows=False, options=R_opts)
print(Rgroups)
Which produces this output:
> {'Core': ['O=C(Cc1ccc([*:3])c(Cl)c1)Nc1cncc2cn([*:1])c([*:2])cc12',
> 'O=C(Cc1ccc([*:3])c(Cl)c1)Nc1cncc2cn([*:1])c([*:2])cc12',
> 'O=C(Cc1ccc([*:3])c(Cl)c1)Nc1cncc2cc([*:1])n([*:2])cc12'], 'R3': ['[H][*:3]',
> 'Cl[*:3]', '[H][*:3]']}
When I roll back to version 2020.03.3, I receive a more intuitive output:
> {'Core': ['O=C(Cc1ccc([*:3])c(Cl)c1)Nc1cncc2c[*:1]:[*:2]cc12',
> 'O=C(Cc1ccc([*:3])c(Cl)c1)Nc1cncc2c[*:1]:[*:2]cc12',
> 'O=C(Cc1ccc([*:3])c(Cl)c1)Nc1cncc2c[*:1]:[*:2]cc12'], 'R1':
> ['c(n:[*:1]):[*:2]', 'c(n:[*:1]):[*:2]', 'c(n:[*:2]):[*:1]'], 'R2':
> ['c(n:[*:1]):[*:2]', 'c(n:[*:1]):[*:2]', 'c(n:[*:2]):[*:1]'], 'R3':
> ['[H][*:3]', 'Cl[*:3]', '[H][*:3]']}
Does anyone know if there’s a setting I can use to receive the old-style
output, or could this be a bug?
Thanks,
Lauren
Dr Lauren Reid
Computational Chemist / Developer
[email protected]
www.medchemica.com
Medchemica Ltd is a company registered in England and Wales with company number
8162245.
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