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. 2003 Mar-Apr;43(2):493-500.
doi: 10.1021/ci025584y.

The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics

Christoph Steinbeck  1 , Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen
Affiliations

The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics

Christoph Steinbeck et al. J Chem Inf Comput Sci. 2003 Mar-Apr.

Abstract

The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.

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Figures

Figure 1
Figure 1
UML diagram, showing the inheritance hierarchy and the dependencies of the fundamental classes within the CDK.
Figure 2
Figure 2
UML diagram, showing the inheritance hierarchy and the dependencies of classes group based on the AtomContainer concept.
Figure 3
Figure 3
Renderer2D and Controller2D cooperating in a simple, CDK-based version of JChemPaint. JChemPaint supports internationalization, with this example showing a dutch interface.
Figure 4
Figure 4
A rings system parsed from a SMILES, analyzed by Figueras’ SSSR algorithm and displayed by the MoleculeViewer class. The process takes 300 ms on a 600 MHz Pentium with Windows XP and JDK 1.3.1.
Figure 5
Figure 5
A CDK code snippet illustrating the use of SmilesParser and StructureDiagramGenerator is shown followed by its output.
See this image and copyright information in PMC

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