R-Group Decomposition with RDKit

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.rdmolops - Molecule Operations

∟R-Group Decomposition with RDKit

This section provides a tutorial example on R-Group decompositions using RGroupDecompose() function in RDKit library.

RDKit library also provides functionalities to perform R-Group decompositions.

r = rdkit.Chem.rdRGroupDecomposition.RGroupDecompose(cs, ms) - Decompose a collecion of molecules into their R-Groups according to given scaffolds. It returns two elements, a list of R-Group of matched molecules and a list of un-matched melecules.

The R-Group of a matched molecule is a dictionary of 'Core', 'R1', 'R2', ..., recording the matched the Core (Scaffold) and sidechains.

Here is a Jupyter Notebook example of performing a R-Group decomposition with just 2 molecules.

from rdkit import Chem
from rdkit.Chem import rdRGroupDecomposition
s = Chem.MolFromSmarts('*Nc1ccc(*)cc1')
ms = list(map(Chem.MolFromSmiles, ['CC(=O)Nc1ccc(O)cc1','CCNc1ccc(OC)cc1']))
gs, _ = rdRGroupDecomposition.RGroupDecompose([s], ms)
l = list(gs[0].values()) + [ms[0]] + list(gs[1].values()) + [ms[1]]
display(rdkit.Chem.Draw.MolsToGridImage(l, subImgSize=(180,180),
  molsPerRow=4))