Cheminformatics Tutorials - Herong's Tutorial Examples - v2.03, by Herong Yang
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
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
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