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The CDK was created by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, then developers of Jmol and JChemPaint, to provide a common code base, on 27-29 September 2000 at the University of Notre Dame. The first source code release was made on 11 May 2011. Since then more than 100 people have contributed to the project, leading to a rich set of functions, as given below. Between 2004 and 2007, CDK News was the project's newsletter of which all articles are available from a public archive. Due to an unsteady rate of contributions, the newsletter was put on hold.
Later, unit testing, code quality checking, and Javadoc validation was introduced. Rajarshi Guha developed a nightly build system, named Nightly, which is still operating at Uppsala University. In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI to generate International Chemical Identifiers (InChIs).
In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.
The CDK is a library, instead of a user program. However, it has been integrated into various environments to make its functions available. CDK is currently used in several applications, including the programming language R, CDK-Taverna (a Taverna workbench plugin),Bioclipse, PaDEL, and Cinfony. Also, CDK extensions exist for Konstanz Information Miner (KNIME) and for Excel, called LICSS ().
In 2008, bits of GPL-licensed code were removed from the library. While those code bits were independent from the main CDK library, and no copylefting was involved, to reduce confusions among users, the ChemoJava project was instantiated.
^Yap, C. W. (2011). "PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints". Journal of Computational Chemistry. 32 (7): 1466-74. doi:10.1002/jcc.21707. PMID21425294.