Molecule Core and Sidechains Decomposition with RDKit

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.rdmolops - Molecule Operations

∟Molecule Core and Sidechains Decomposition with RDKit

This section provides a tutorial example on decomposing a molecule into a core substructure and its sidechains using RDKit library.

RDKit library also provides functionalities to decompose a molecule into a core substructure and its sidechains.

n = rdkit.Chem.rdmolops.ReplaceCore(m, s) - Removes a substructure as the core of a molecule and labels the sidechains with dummy atoms.

n = rdkit.Chem.rdmolops.ReplaceSidechains(m, s) - Replaces sidechains of a substructure in a molecule with dummy atoms for their attachment points.

Here is a Jupyter Notebook example of decomposing molecule into a core substructure and its sidechains.

import rdkit.Chem
m = rdkit.Chem.MolFromSmiles('CC(=O)Nc1ccc(O)cc1')
p = rdkit.Chem.MolFromSmiles('Nc1ccccc1')
rdkit.Chem.AllChem.Compute2DCoords(p)
rdkit.Chem.AllChem.GenerateDepictionMatching2DStructure(m, p)
rdkit.Chem.Draw.MolsToGridImage([p, m], subImgSize=(200,200))

c = rdkit.Chem.ReplaceSidechains(m, p)
s = rdkit.Chem.ReplaceCore(m, p)
rdkit.Chem.Draw.MolsToGridImage([c, s], subImgSize=(200,200))