Tutorials

Clustering conformers

Tutorial on how to cluster molecular conformers.

PUBLISHED - Nov 2, 2023

One common workflow in conformational analysis is to generate a bunch of conformers for a molecule and then find a representative subset by clustering them. The RDKit has everything required to do this, but there's not all that much info out there showing how to do it.

This blog post aims to change that.

from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
from rdkit import Chem
from rdkit.Chem import rdDistGeom
from rdkit.Chem import rdMolAlign
import rdkit
print(rdkit.__version__)

# modified CHEMBL12747, ionized
m = Chem.MolFromSmiles('O=C([O-])CCn1c(=O)c(=O)[nH]c2cc([N+](=O)[O-])c(-n3ccc(C=NOCc4ccccc4)c3)cc21')

Generate conformers

Start by constructing a molecule and then generating a set of 300 conformers for it using ETKDGv3.