RDKit Installation Options

This section provides a quick introduction of RDKit installation options: Python library with Anaconda, Binary Package for CentOS, Build from source code.

There are several options to install RDKit on your computer.

1. Install RDKit Python Library with Anaconda - This is the easiest and fastest way to install RDKit. You have to access RDKit functionalities with Python scripts in an Anaconda environment.

2. Install RDKit binary packages - This requires you to find a binary package that matches your computer architecture and system. Once installed, you can access RDKit functionalities using "rdkit ..." commands.

3. Install RDKit from Source Code - This requires you to have C++ compiler and build tools. You also have to resolve potential compatibility and dependency issues with other libraries. But this gives you the possibility to install it on any computer.

I have tried all options as shown in next tutorials.

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

 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

 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