Chemistry Development Kit

Short description: Computer software

Chemistry Development Kit

Original author(s)| Christoph Steinbeck, Egon Willighagen, Dan Gezelter
Developer(s)| The CDK Project
Initial release| 11 May 2001; 24 years ago (2001-05-11)[1]
Stable release| 2.8[2] (September 14, 2022; 3 years ago (2022-09-14)) [±]
Repository| github.com/cdk/cdk
Written in| Java
Operating system| Windows, Linux, Unix, macOS
Platform| IA-32, x86-64
Available in| English
Type| Chemoinformatics, molecular modelling, bioinformatics
License| LGPL 2.0
Website| cdk.github.io

The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics.[3][4] 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.

## Contents

* 1 History
* 2 Library
* 3 Major features
* 3.1 Chemoinformatics
* 3.2 Bioinformatics
* 3.3 General
* 4 See also
* 5 References
* 6 External links

## 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.[5] Since then more than 100 people have contributed to the project,[6] 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.[7] Due to an unsteady rate of contributions, the newsletter was put on hold.

CDK News Language| English

|

Edited by| Egon Willighagen, Christoph Steinbeck
Publication details
History| 2004-2007
Standard abbreviations
ISO 4 (alt) * Bluebook (alt1 * alt2)
NLM (alt) * MathSciNet (alt )
ISO 4| CDK News
Indexing
CODEN * JSTOR (alt) * LCCN (alt)
MIAR * NLM (alt) * Scopus
ISSN| 1614-7553

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.[8] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[9] to generate International Chemical Identifiers (InChIs).[10] In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.[11]

## 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,[12] CDK-Taverna (a Taverna workbench plugin),[13] Bioclipse, PaDEL,[14] and Cinfony.[15] Also, CDK extensions exist for Konstanz Information Miner (KNIME)[16] and for Excel, called LICSS ([1]).[17]

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.[18]

## Major features

### Chemoinformatics

* 2D molecule editor and generator
* 3D geometry generation
* ring finding[19][20]
* substructure search using exact structures and Smiles arbitrary target specification (SMARTS) like query language
* QSAR descriptor calculation[21]
* fingerprint calculation, including the ECFP and FCFP fingerprints[22]
* force field calculations
* many input-output chemical file formats, including simplified molecular-input line-entry system (SMILES), Chemical Markup Language (CML), and chemical table file (MDL)
* structure generators[23]
* International Chemical Identifier support, via JNI-InChI

### Bioinformatics

* protein active site detection
* cognate ligand detection[24]
* metabolite identification[25]
* pathway databases
* 2D and 3D protein descriptors[26]

### General

* Python wrapper; see Cinfony
* Ruby wrapper
* active user community

## See also

* Bioclipse – an Eclipse–RCP based chemo-bioinformatics workbench
* Blue Obelisk
* JChemPaint – Java 2D molecule editor, applet and application
* Jmol – Java 3D renderer, applet and application
* JOELib – Java version of Open Babel, OELib
* List of free and open-source software packages
* List of software for molecular mechanics modeling

## References

1. ↑ "The Chemistry Development Kit - Browse /OldFiles at SourceForge.net". https://sourceforge.net/projects/cdk/files/OldFiles/.
2. ↑ "cdk/cdk: CDK 2.8". ZENODO. 2022-09-14. doi:10.5281/zenodo.7079512.
3. ↑ Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. L. (2003). "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. doi:10.1021/ci025584y. PMID 12653513.
4. ↑ Willighagen, Egon L.; Mayfield, John W.; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš et al. (2017-06-06). "The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching" (in En). Journal of Cheminformatics 9 (1): 33. doi:10.1186/s13321-017-0220-4. ISSN 1758-2946. PMID 29086040.
5. ↑ "The Chemistry Development Kit - Browse /OldFiles at SourceForge.net". http://sourceforge.net/projects/cdk/files/OldFiles/.
6. ↑ "The Chemistry Development Kit (CDK)". 12 October 2021. https://github.com/cdk/cdk/blob/master/AUTHORS.txt.
7. ↑ "The Chemistry Development Kit - Browse /CDK News at SourceForge.net". https://sourceforge.net/projects/cdk/files/CDK News/.
8. ↑ "CDK 1.5.x Nightly Build - 2013-05-10 (21:21) [Commit 2abcb5d61304e58d55ea26a23ebd0d375deea36d]". http://pele.farmbio.uu.se/nightly/. Retrieved 2013-08-05.
9. ↑ "Home". http://jni-inchi.sourceforge.net/.
10. ↑ Spjuth, O.; Berg, A.; Adams, S.; Willighagen, E. L. (2013). "Applications of the InChI in cheminformatics with the CDK and Bioclipse". Journal of Cheminformatics 5 (1): 14. doi:10.1186/1758-2946-5-14. PMID 23497723.
11. ↑ "John May is now release manager of CDK 1.5.x". http://chem-bla-ics.blogspot.nl/2013/04/john-may-is-now-release-manager-of-cdk.html.
12. ↑ Guha, R. (2007). "Chemical informatics functionality in R". Journal of Statistical Software 18 (5): 1–16. doi:10.18637/jss.v018.i05.
13. ↑ Kuhn, T.; Willighagen, E. L.; Zielesny, A.; Steinbeck, C. (2010). "CDK-Taverna: an open workflow environment for cheminformatics". BMC Bioinformatics 11: 159. doi:10.1186/1471-2105-11-159. PMID 20346188.
14. ↑ 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. PMID 21425294.
15. ↑ O'Boyle, Noel M (2008). "Cinfony – combining Open Source cheminformatics toolkits behind a common interface". Chemistry Central Journal 2 (1): 24. doi:10.1186/1752-153X-2-24. PMID 19055766.
16. ↑ Beisken, S.; Meinl, T.; Wiswedel, B.; De Figueiredo, L. F.; Berthold, M.; Steinbeck, C. (2013). "KNIME-CDK: Workflow-driven Cheminformatics". BMC Bioinformatics 14: 257. doi:10.1186/1471-2105-14-257. PMID 24103053.
17. ↑ Lawson, K. R.; Lawson, J. (2012). "LICSS - a chemical spreadsheet in microsoft excel". Journal of Cheminformatics 4 (1): 3. doi:10.1186/1758-2946-4-3. PMID 22301088.
18. ↑ ChemoJava
19. ↑ Berger, Franziska; Flamm, Christoph; Gleiss, Petra M.; Leydold, Josef; Stadler, Peter F. (March 2004). "Counterexamples in Chemical Ring Perception". Journal of Chemical Information and Computer Sciences 44 (2): 323–331. doi:10.1021/ci030405d. PMID 15032507. http://ul.qucosa.de/api/qucosa:33096/attachment/ATT-0/.
20. ↑ May, John W; Steinbeck, Christoph (2014). "Efficient ring perception for the Chemistry Development Kit". Journal of Cheminformatics 6 (1): 3. doi:10.1186/1758-2946-6-3. PMID 24479757.
21. ↑ Steinbeck, C.; Hoppe, C.; Kuhn, S.; Floris, M.; Guha, R.; Willighagen, E. L. (2006). "Recent developments of the chemistry development kit (CDK) — an open-source java library for chemo- and bioinformatics". Curr. Pharm. Des. 12 (17): 2111–20. doi:10.2174/138161206777585274. PMID 16796559. http://www.benthamdirect.org/pages/content.php?CPD/2006/00000012/00000017/0005B.SGM.
Guangli, M.; Yiyu, C. (2006). "Predicting Caco-2 permeability using support vector machine and chemistry development kit". J Pharm Pharm Sci 9 (2): 210–21. PMID 16959190. https://www.ualberta.ca/~csps/JPPS9_2/Dr_Guangli/MS_538.htm.
22. ↑ Clark, Alex M; Sarker, Malabika; Ekins, Sean (2014). "New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0". Journal of Cheminformatics 6: 38. doi:10.1186/s13321-014-0038-2. PMID 25302078.
23. ↑ Peironcely, J. E.; Rojas-Chertó, M.; Fichera, D.; Reijmers, T.; Coulier, L.; Faulon, J. L.; Hankemeier, T. (2012). "OMG: Open molecule generator". Journal of Cheminformatics 4 (1): 21. doi:10.1186/1758-2946-4-21. PMID 22985496.
24. ↑ Bashton, M.; Nobeli, I.; Thornton, J. M. (2006). "Cognate Ligand Domain Mapping for Enzymes". Journal of Molecular Biology 364 (4): 836–52. doi:10.1016/j.jmb.2006.09.041. PMID 17034815.
25. ↑ Rojas-Cherto, M.; Kasper, P. T.; Willighagen, E. L.; Vreeken, R. J.; Hankemeier, T.; Reijmers, T. H. (2011). "Elemental composition determination based on MSn". Bioinformatics 27 (17): 2376–2383. doi:10.1093/bioinformatics/btr409. PMID 21757467.
26. ↑ Ruiz-Blanco, Yasser B; Paz, Waldo; Green, James; Marrero-Ponce, Yovani (2015). "ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins". BMC Bioinformatics 16: 162. doi:10.1186/s12859-015-0586-0. PMID 25982853.

## External links

* CDK Wiki – the community wiki
* Planet CDK \- a blog planet
* CDK Depict
* OpenScience.org

* v
* t
* e

Computational chemistry software

Cheminformatics|

| Open-source|

* Avalon Cheminformatics Toolkit
* Bioclipse
* Blue Obelisk
* Chemistry Development Kit
* ECCE
* JOELib
* OELib
* Open Babel
* RDKit

|

Proprietary|

* Canvas
* Chemicalize
* Discovery Studio

Chemical kinetics|

| Open-source|

* APBS
* Cantera
* KPP

|

Proprietary|

* Autochem
* Chemical WorkBench
* CHEMKIN
* COSILAB
* DelPhi
* Khimera

Molecular modelling and visualization|

List of molecular graphics systems

| Open-source|

* Ascalaph Designer
* Avogadro
* BALL
* Biskit
* CPMD
* Gabedit
* Ghemical
* Jmol
* Molekel
* PyMOL
* QuteMol
* RasMol

|

Proprietary|

* Abalone
* ACD/ChemSketch
* Atomistix ToolKit
* ChemDraw
* EzMol
* Gaussian
* Maestro
* MarvinSketch
* MarvinView
* MODELLER
* Molecular Operating Environment
* Spartan
* UCSF Chimera
* VMD

Molecular docking|

List of protein-ligand docking software

| Open-source|

* AutoDock
* AutoDock Vina
* FlexAID
* rDock

|

Proprietary|

* Glide
* Molecular Operating Environment

Molecular dynamics|

| Open-source|

* GROMACS
* LAMMPS
* OpenMM
* PLUMED

|

Proprietary|

* Abalone
* AMBER
* CHARMM
* Desmond
* GROMOS
* NAMD

Quantum chemistry|

List of quantum chemistry and solid-state physics software

| Open-source|

* ABINIT
* ACES (CFOUR)
* AIMAll
* BigDFT
* CP2K
* DACAPO
* Dalton
* DP code
* FreeON
* HORTON
* MADNESS
* MPQC
* NWChem
* Octopus
* PSI
* PyQuante
* PySCF
* Quantum ESPRESSO (PWscf)
* RMG
* SAMSON
* SIESTA
* VB2000
* YAMBO code

|

Proprietary|

* ADF
* AMPAC
* DMol3
* CADPAC
* CASINO
* CASTEP
* COLUMBUS
* CONQUEST
* CPMD
* CRUNCH
* CRYSTAL
* DIRAC
* Firefly
* GAMESS (UK)
* GAMESS (US)
* Gaussian
* Jaguar
* MOLCAS
* MOLPRO
* MOPAC
* ONETEP
* OpenAtom
* ORCA
* PARSEC
* PLATO
* PQS
* Q-Chem
* Quantemol
* Scigress
* Spartan
* TeraChem
* TURBOMOLE
* VASP
* WIEN2k
* XMVB

Skeletal structure drawing|

| Open-source|

* BKChem
* JChemPaint
* JME Molecule Editor
* Molsketch
* XDrawChem

|

Proprietary|

* ACD/ChemSketch
* ChemDoodle
* ChemDraw
* MarvinSketch

Others|

* Aqion
* Eulim
* EXC code
* GenX
* GSim
* ICM (ICM-Browser)
* Materials Studio
* Molden
* OpenChrom
* RubyChem
* SASHIMI

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