Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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))
Table of Contents
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.Chem.rdmolops - Molecule Operations
What Is rdkit.Chem.rdmolops Module
Molecule Similarity Based on Fingerprints with RDKit
►Molecule Core and Sidechains Decomposition with RDKit
R-Group Decomposition with RDKit
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction