Chemistry Development Kit

The Chemistry Development Kit is an open source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS. It is distributed under the GNU LGPL.

History
The CDK was created in 2000 by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, the developers of Jmol and JChemPaint, to provide a common code base.

Chemoinformatics

 * 2D diagram editing and generation
 * 3D geometry generation
 * substructure search using exact structures and SMARTS-like queries
 * QSAR descriptor calculation (e.g. )
 * fingerprint calculation
 * force field calculations
 * many chemical input/output formats
 * structure generators

Bioinformatics

 * protein active site detection
 * cognate ligand detection

General

 * Python wrapper
 * Ruby wrapper
 * active user community
 * newsletter: CDK News