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:

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))
rdkit.Chem.rdFMCS - Maximum Common Substructure
rdkit.Chem.rdFMCS - Maximum Common Substructure

For more information on MCS with RDKit, see "T006 · Maximum common substructure" at https://projects.volkamerlab.org/teachopencadd/index.html.

Table of Contents

 About This Book

 SMILES (Simplified Molecular-Input Line-Entry System)

 Open Babel: The Open Source Chemistry Toolbox

 Using Open Babel Command: "obabel"

 Generating SVG Pictures with Open Babel

 Substructure Search with Open Babel

 Similarity Search with Open Babel

 Fingerprint Index for Fastsearch with Open Babel

 Stereochemistry with Open Babel

 Command Line Tools Provided by Open Babel

 RDKit: Open-Source Cheminformatics Software

 rdkit.Chem.rdchem - The Core Module

 rdkit.Chem.rdmolfiles - Molecular File Module

 rdkit.Chem.rdDepictor - Compute 2D Coordinates

 rdkit.Chem.Draw - Handle Molecule Images

Molecule Substructure Search with RDKit

 RDKit m.HasSubstructMatch(s) - Substructure Match

 RDKit GenerateDepictionMatching2DStructure(m, s) - Substructure Orientation

 RDKit rdMolDraw2D.PrepareAndDrawMolecule - Substructure Highlight

 RDKit Substructure Search with SMARTS

rdkit.Chem.rdFMCS - Maximum Common Substructure

 rdkit.Chem.rdSubstructLibrary - Substructure Library

 Substructure Library in Binary and SMILES Formats

 rdkit.Chem.rdmolops - Molecule Operations

 RDKit Performance on Substructure Search

 OCSR (Optical Chemical Structure Recognition)

 AlphaFold - Protein Structure Prediction

 Resources and Tools

 Cheminformatics Related Terminologies


 Full Version in PDF/EPUB