RDKit: Open-Source Cheminformatics Software

This chapter provides introductions and tutorial examples on RDKit, an open-source cheminformatics software. Topics include installing options; install RDKit Python library with Anaconda; trying to find RDKit binary package for CentOS systems; building RDKit from source code; testing RDKit C++ API; trying to connect Python API to RDKit native code.

What Is RDKit

RDKit Installation Options

Install RDKit in an Anaconda Environment

Install RDKit Binary Package for CentOS

Build RDKit from Source Code on CentOS System

Compile, Link and Run RDKit C++ API Examples

Try Python API with RDKit Native Code


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


 Full Version in PDF/EPUB