rdkit.Chem.rdchem - The Core Module

This chapter provides introductions and tutorial examples on rdkit.Chem.rdchem module. Topics include introduction of rdkit.Chem.rdchem module and its main classes: Mol, Atom, Bond, RWMol.

What Is rdkit.Chem.rdchem Module

rdkit.Chem.rdchem.Mol - The Molecule Class

rdkit.Chem.rdchem.Atom - The Atom Class

rdkit.Chem.rdchem.Bond - The Bond Class

rdkit.Chem.rdchem.RWMol - The RWMol Class

Takeaways:

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.Chem.rdmolops - Molecule Operations

 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

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB