Chemistry Development Kit Explained

Chemistry Development Kit
Logo Alt:Burgundy-colored ball and stick pseudo-molecule diagram spelling the three letters C, D, and K.
Author:Christoph Steinbeck, Egon Willighagen, Dan Gezelter
Developer:The CDK Project
Released:[1]
Programming Language:Java
Operating System:Windows, Linux, Unix, macOS
Platform:IA-32, x86-64
Language:English
Genre:Chemoinformatics, molecular modelling, bioinformatics
License:LGPL 2.0

The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics.[2] [3] It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.

History

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.[4] Since then more than 100 people have contributed to the project,[5] 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.[6] Due to an unsteady rate of contributions, the newsletter was put on hold.

CDK News
Abbreviation:CDK News
Language:English
History:2004-2007
Issn:1614-7553
Italic Title:no

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.[7] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[8] to generate International Chemical Identifiers (InChIs).[9] In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.[10]

Library

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,[11] CDK-Taverna (a Taverna workbench plugin),[12] Bioclipse, PaDEL,[13] and Cinfony.[14] Also, CDK extensions exist for Konstanz Information Miner (KNIME)[15] and for Excel, called LICSS (https://github.com/KevinLawson/excel-cdk).[16]

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.[17]

Major features

Chemoinformatics

Bioinformatics

General

See also

External links

Notes and References

  1. Web site: The Chemistry Development Kit - Browse /OldFiles at SourceForge.net.
  2. Steinbeck . C. . Han . Y. Q. . Kuhn . S. . Horlacher . O. . Luttmann . E. . Willighagen . E. L. . The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics . Journal of Chemical Information and Computer Sciences . 43 . 2 . 493–500 . 2003 . 12653513 . 10.1021/ci025584y . 4901983 .
  3. Willighagen. Egon L.. Mayfield. John W.. Alvarsson. Jonathan. Berg. Arvid. Carlsson. Lars. Jeliazkova. Nina. Kuhn. Stefan. Pluskal. Tomáš. Rojas-Chertó. Miquel. 2017-06-06. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics. En. 9. 1. 33. 10.1186/s13321-017-0220-4. 29086040. 5461230. 1758-2946 . free .
  4. Web site: The Chemistry Development Kit - Browse /OldFiles at SourceForge.net.
  5. Web site: The Chemistry Development Kit (CDK). GitHub. 12 October 2021.
  6. Web site: The Chemistry Development Kit - Browse /CDK News at SourceForge.net.
  7. Web site: CDK 1.5.x Nightly Build - 2013-05-10 (21:21) [Commit 2abcb5d61304e58d55ea26a23ebd0d375deea36d] . 2013-08-05 . dead . https://web.archive.org/web/20130524042151/http://pele.farmbio.uu.se/nightly/ . 2013-05-24 .
  8. Web site: Home . jni-inchi.sourceforge.net.
  9. Spjuth . O. . Berg . A. . Adams . S. . Willighagen . E. L. . Applications of the InChI in cheminformatics with the CDK and Bioclipse . 10.1186/1758-2946-5-14 . Journal of Cheminformatics . 5 . 1 . 14 . 2013 . 23497723 . 3674901 . free .
  10. Web site: John May is now release manager of CDK 1.5.x.
  11. Guha . R. . Chemical informatics functionality in R . Journal of Statistical Software . 18 . 5 . 1–16 . 2007 . 10.18637/jss.v018.i05. free .
  12. Kuhn . T. . Willighagen . E. L. . Zielesny . A. . Steinbeck . C. . CDK-Taverna: an open workflow environment for cheminformatics . BMC Bioinformatics . 11 . 159 . 2010 . 20346188 . 2862046 . 10.1186/1471-2105-11-159 . free .
  13. 10.1002/jcc.21707 . 21425294 . PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints . Journal of Computational Chemistry . 32 . 7 . 1466–74 . 2011 . Yap . C. W. . 206032727 . free .
  14. 10.1186/1752-153X-2-24 . 19055766 . 2646723 . Cinfony – combining Open Source cheminformatics toolkits behind a common interface . Chemistry Central Journal . 2008 . 2 . 1 . 24 . Noel M . O'Boyle . free .
  15. Beisken . S. . Meinl . T. . Wiswedel . B. . De Figueiredo . L. F. . Berthold . M. . Steinbeck . C. . 10.1186/1471-2105-14-257 . KNIME-CDK: Workflow-driven Cheminformatics . BMC Bioinformatics . 14 . 257 . 2013 . 24103053 . 3765822 . free .
  16. Lawson . K. R. . Lawson . J. . 10.1186/1758-2946-4-3 . LICSS - a chemical spreadsheet in microsoft excel . Journal of Cheminformatics . 4 . 1 . 3 . 2012 . 22301088 . 3310842 . free .
  17. https://github.com/egonw/chemojava ChemoJava
  18. Berger. Franziska. Flamm. Christoph. Gleiss. Petra M.. Leydold. Josef. Stadler. Peter F.. Counterexamples in Chemical Ring Perception. Journal of Chemical Information and Computer Sciences. March 2004. 44. 2. 323–331. 10.1021/ci030405d. 15032507.
  19. May. John W. Steinbeck. Christoph. Efficient ring perception for the Chemistry Development Kit. Journal of Cheminformatics. 2014. 6. 1. 3. 10.1186/1758-2946-6-3. 24479757. 3922685 . free .
  20. Steinbeck . C. . Hoppe . C. . Kuhn . S. . Floris . M. . Guha . R. . Willighagen . E. L. . Recent developments of the chemistry development kit (CDK) — an open-source java library for chemo- and bioinformatics . Curr. Pharm. Des. . 12 . 17 . 2111–20 . 2006 . 16796559 . 10.2174/138161206777585274 . dead . https://web.archive.org/web/20110725062137/http://www.benthamdirect.org/pages/content.php?CPD%2F2006%2F00000012%2F00000017%2F0005B.SGM . 2011-07-25 . 2066/35445 . free .
    Guangli . M. . Yiyu . C. . Predicting Caco-2 permeability using support vector machine and chemistry development kit . J Pharm Pharm Sci . 9 . 2 . 210–21 . 2006 . 16959190 .
  21. Clark . Alex M . Sarker . Malabika . Malabika Sarker . Ekins . Sean . 2014 . New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0 . Journal of Cheminformatics . 6 . 38 . 10.1186/s13321-014-0038-2 . 4190048 . 25302078 . free .
  22. Peironcely . J. E. . Rojas-Chertó . M. . Fichera . D. . Reijmers . T. . Coulier . L. . Faulon . J. L. . Hankemeier . T. . 10.1186/1758-2946-4-21 . OMG: Open molecule generator . Journal of Cheminformatics . 4 . 1 . 21 . 2012 . 22985496 . 3558358 . free .
  23. 10.1016/j.jmb.2006.09.041 . Bashton . M. . Nobeli . I. . Thornton . J. M. . Cognate Ligand Domain Mapping for Enzymes . Journal of Molecular Biology . 364 . 4 . 836–52 . 2006 . 17034815. free .
  24. Rojas-Cherto . M. . Kasper . P. T. . Willighagen . E. L. . Vreeken . R. J. . Hankemeier . T. . Reijmers . T. H. . 10.1093/bioinformatics/btr409 . Elemental composition determination based on MSn . Bioinformatics . 27 . 17 . 2376–2383 . 2011 . 21757467 . free .
  25. 10.1186/s12859-015-0586-0 . ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins . BMC Bioinformatics . 16 . 162 . 2015 . Ruiz-Blanco . Yasser B . Paz . Waldo . Green . James . Marrero-Ponce . Yovani . 25982853 . 4432771 . free .

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Chemistry Development Kit".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.