Chemistry Development Kit
| Company type | Open-source software project |
|---|---|
| Industry | Chemoinformatics, Bioinformatics, Software |
| Founded | May 11, 2001 |
| Founder | Christoph Steinbeck, Egon Willighagen, Dan Gezelter |
Area served | Worldwide |
Key people | Rajarshi Guha, John Mayfield |
| Products | Chemoinformatics and bioinformatics software toolkit |
| Owner | Community-driven open-source project |
Number of employees | Over 100 contributors (developers) (Since inception (2001–present)) |
| Website | cdk |
The Chemistry Development Kit (CDK) is an open-source software toolkit written in Java, designed for applications in chemoinformatics and bioinformatics. It operates across multiple operating systems, including Windows, Linux, Unix, and macOS, and is available under the GNU Lesser General Public License (LGPL) version 2.0.
History
Initiated by Christoph Steinbeck, Egon Willighagen, and Dan Gezelter—who were also involved in developing Jmol and JChemPaint—the CDK project began during a 2000 gathering at the University of Notre Dame with the goal of establishing a unified codebase. The initial source code was publicly released on 11 May 2001. Since its inception, the project has grown through contributions from over 100 developers, enhancing its capabilities for molecular modeling and cheminformatics tasks. From 2004 until 2007, the team issued CDK News, a newsletter that has since been archived due to varying levels of contributor activity.
Subsequent advancements incorporated unit testing, verification of code quality, and validation of Javadoc documentation. Rajarshi Guha set up an automated nightly build system hosted at Uppsala University. In 2012, CDK officially aligned with the InChI Trust, incorporating JNI-InChI to facilitate the generation of International Chemical Identifiers (InChIs), thereby improving chemical data interoperability. In April 2013, John Mayfield joined the team as a release manager to supervise development branches.
Library
Rather than functioning as a standalone application, the CDK serves as a programming library that has been embedded within various platforms to broaden its utility. It is integrated into tools such as the programming language R, CDK-Taverna (a plugin for the Taverna workbench), Bioclipse, PaDEL, and Cinfony. Additional extensions connect CDK functionalities with Konstanz Information Miner (KNIME) and Microsoft Excel through LICSS.
In 2008, portions of the code licensed under GPL were extracted from CDK to reduce licensing complexity for users, which led to the formation of the ChemoJava initiative.
Chemoinformatics
- Generation and editing of 2D molecular structures
- Construction of 3D molecular geometries
- Algorithms for ring detection
- Substructure searching using exact matches and SMARTS queries
- Computation of QSAR descriptors
- Calculation of molecular fingerprints, including ECFP and FCFP types
- Force field computations for molecular modeling
- Compatibility with numerous chemical file formats such as SMILES, Chemical Markup Language (CML), and MDL files
- Tools for structure generation
- Support for International Chemical Identifiers through JNI-InChI
Bioinformatics
- Detection of protein active sites
- Identification of cognate ligands
- Metabolite recognition
- Access to pathway databases
- Calculation of both 2D and 3D protein descriptors
General
- Availability of a Python interface via Cinfony
- A wrapper for Ruby
- An engaged and active user community
See also
- Bioclipse – A chemo-bioinformatics workbench based on Eclipse–RCP
- Blue Obelisk
- JChemPaint – Java-based 2D molecule editor available as both applet and standalone application
- Jmol – Java-based 3D molecular viewer provided as applet and application
- JOELib – Java implementation similar to Open Babel and OELib
- List of free and open-source software packages
- List of software for molecular mechanics modeling
External links
- CDK Wiki – collaborative community wiki
- Planet CDK – blog collection platform
- CDK Depict
- OpenScience.org