rdkit.Chem.rdFMCS - Maximum Common Substructure

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Molecule Substructure Search with RDKit

∟rdkit.Chem.rdFMCS - Maximum Common Substructure

This section provides a quick introduction on rdkit.Chem.rdFMCS module in RDKit library that provides functionalities to find the MCS (Maximum Common Substructure) of a set of molecules.

What Is rdkit.Chem.rdFMCS Module? rdkit.Chem.rdFMCS module in RDKit library provides functionalities to find the MCS (Maximum Common Substructure) of a set of molecules.

rdkit.Chem.rdFMCS module contains one main method and one main class:

r = rdkit.Chem.rdFMCS.FindMCS(ms) - Finds the MCS for a set of molecules and returns it as a rdkit.Chem.rdFMCS.MCSResult object. This method uses the following algorithm:

best_substructure = None
pick one structure in the set as query, all other as targets
for each substructure in the query:
    convert into a SMARTS string based on the desired match properties
    if SMARTS pattern exists in all of the targets:
        then it is a common substructure
        keep track of the maximum of such substructure

rdkit.Chem.rdFMCS.MCSResult - Represents the MCS returned from the FindMCS() method. It contains the following properties:

r.canceled - If True, the MCS calculation did not finish
r.numAtoms - Number of atoms in MCS
r.numBonds - Number of bonds in MCS
r.queryMol - Query molecule for the MCS
r.smartsString - SMARTS string for the MCS

Here is a nice short Jupyter Notebook example of finding the MCS using RDKit library.

import rdkit.Chem
ms = ["CCC1CC2C1CN2", "C1CC2C1CC2"]
ms = list(map(rdkit.Chem.MolFromSmiles, ms))
i = rdkit.Chem.Draw.MolsToGridImage(ms, subImgSize=(150,150))
r = rdkit.Chem.rdFMCS.FindMCS(ms)
display(i, r.smartsString)
rdkit.Chem.Draw.MolToImage(r.queryMol, size=(120,120))