Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
What Is RDKit
This section provides a quick introduction of RDKit, a collection of cheminformatics and machine-learning software written in C++ and Python.
What Is RDKit - RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
The current release supports the following packages:
rdkit.Avalon package rdkit.Chem package rdkit.Chem.AtomPairs package rdkit.Chem.ChemUtils package rdkit.Chem.Draw package rdkit.Chem.EState package rdkit.Chem.FeatMaps package rdkit.Chem.Features package rdkit.Chem.Fingerprints package rdkit.Chem.Fraggle package rdkit.Chem.MolDb package rdkit.Chem.MolKey package rdkit.Chem.Pharm2D package rdkit.Chem.Pharm3D package rdkit.Chem.Scaffolds package rdkit.Chem.SimpleEnum package rdkit.Chem.Subshape package rdkit.Chem.Suppliers package rdkit.Chem.fmcs package rdkit.DataManip package rdkit.DataStructs package rdkit.Dbase package rdkit.DistanceGeometry package rdkit.ForceField package rdkit.Geometry package rdkit.ML package rdkit.ML.Cluster package rdkit.ML.Composite package rdkit.ML.Data package rdkit.ML.DecTree package rdkit.ML.Descriptors package rdkit.ML.InfoTheory package rdkit.ML.KNN package rdkit.ML.MLUtils package rdkit.ML.ModelPackage package rdkit.ML.NaiveBayes package rdkit.ML.Neural package rdkit.ML.SLT package rdkit.ML.Scoring package rdkit.Numerics package rdkit.SimDivFilters package rdkit.VLib package rdkit.utils package
For more information, visit RDKit Website at http://www.rdkit.org.
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