RDKit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

BSD license - a business friendly license for open source
Core data structures and algorithms in C++
Python (2.x and 3.x) wrapper generated using Boost.Python
Java and C# wrappers generated with SWIG
2D and 3D molecular operations
Descriptor and Fingerprint generation for machine learning
Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
Cheminformatics nodes for KNIME
Contrib folder with useful community-contributed software harnessing the power of the RDKit

Web presence

Available on the RDKit page and in the Docs folder on GitHub

Installation instructions are available in Docs/Book/Install.md.

Windows binaries are available with each release.
RPMs for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
homebrew formula for building on the Mac. Contributed by Eddie Cao.
recipes for building using the excellent conda package manager. Contributed by Riccardo Vianello.

ChEMBL Beaker - standalone web server wrapper for RDKit and OSRA
myChEMBL (blog post, paper) - A virtual machine implementation of open data and cheminformatics tools
sdf_viewer.py - an interactive SDF viewer
sdf2ppt - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation.
MolGears - A cheminformatics tool for bioactive molecules
PYPL - Simple cartridge that lets you call Python scripts from Oracle PL/SQL.
shape-it-rdkit - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend
WONKA - Tool for analysis and interrogation of protein-ligand crystal structures
OOMMPPAA - Tool for directed synthesis and data analysis based on protein-ligand crystal structures
DeepChem - Machine learning library for small molecules

Code released under the BSD license.