Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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.
Install RDKit in an Anaconda Environment
Install RDKit Binary Package for CentOS
Build RDKit from Source Code on CentOS System
Takeaways:
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
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