Readers of this book will probably know what the Chemistry Development Kit (CDK) is: An Open-Source Java Library for Chemo- and Bioinformatics [1]. While the CDK project was founded in 2000, the code base originates from the groundbreaking open source cheminformatics work Christoph Steinbeck started in 1997 with the JChemPaint [2] and CompChem projects.

This book is not about those past projects, however; it is about the CDK as it is now. It has evolved enormously over the past 10 years, and got more and more functionality [3,4], thanx to the many contributors (see the Author List). Moreover, by now, the CDK has shown its role in many cheminformatics and bioinformatics fields, and you will find that this book cites many scientific papers that use the CDK.

The goal of this book is to introduce the reader, you, to the wide variety of functionality available in the library. It will discuss parts of the data model, basic cheminformatics algorithms, chemical file formats, as well as some of the applications of the CDK.

During the discussion of the various features, we will also discuss some of the important cheminformatics concepts, but in a minimal way only. The goal of this book is not to provide an introduction into cheminformatics. For that, various other books are available [5,6,7,8,9].

As such, this book does require a basic chemical education. It assumes that you know what atoms are, how they are connected by chemical bonds, and it assumes some basic computer knowledge. This book is about learning how to perform cheminformatics tasks using the CDK. But to keep the required knowledge to a minimum, the examples will be pretty verbose.


  1. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E. The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. JCICS. 2003 Feb 11;43(2):493–500. doi:10.1021/CI025584Y (Scholia)
  2. Krause S, Willighagen E, Steinbeck C. JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures. Molecules. 2000 Jan 28;5(1):93–8. doi:10.3390/50100093 (Scholia)
  3. Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen E. Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Curr Pharm Des [Internet]. 2006 Jun 1;12(17):2111–20. Available from: doi:10.2174/138161206777585274 (Scholia)
  4. Willighagen E, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, et al. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform. 2017 Jun 6;9(1). doi:10.1186/S13321-017-0220-4 (Scholia)
  5. Gasteiger J, Engel T, editors. Chemoinformatics: A Textbook. Weinheim, Deutschland: Wiley-VCH; 2003.
  6. Leach AR, Gillet VJ. An introduction to chemoinformatics. Berlin, Deutschland: Springer Science+Business Media; 2007.
  7. Faulon J-L, Bender A, editors. Handbook of Chemoinformatics Algorithms. 2010.
  8. Wikberg J, Eklund M, Willighagen E, Spjuth O, Lapins M, Engkvist O, et al. Introduction to Pharmaceutical Bioinformatics. 2018.
  9. Wild DJ. Introducing Cheminformatics [Internet]. 2013. Available from: