Chemistry Development Kit
Encyclopedia
The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics
. It is available for Windows
, Unix
, and Mac OS
. It is distributed under the GNU LGPL.
and JChemPaint
at the time, to provide a common code base, on 27–29 September 2000 at the University of Notre Dame
. Since then many people have contributed to the project, leading to a rich set of functionality, as given below.
, CDK-Taverna (a Taverna workbench
plugin), Bioclipse
, and Cinfony. Additionally, CDK extensions exist for KNIME
and Excel
(excel-cdk).
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.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. It is available for Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Unix
Unix
Unix is a multitasking, multi-user computer operating system originally developed in 1969 by a group of AT&T employees at Bell Labs, including Ken Thompson, Dennis Ritchie, Brian Kernighan, Douglas McIlroy, and Joe Ossanna...
, and Mac OS
Mac OS
Mac OS is a series of graphical user interface-based operating systems developed by Apple Inc. for their Macintosh line of computer systems. The Macintosh user experience is credited with popularizing the graphical user interface...
. It is distributed under the GNU LGPL.
History
The CDK was created by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, the developers of JmolJmol
Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
and JChemPaint
JChemPaint
JChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems...
at the time, to provide a common code base, on 27–29 September 2000 at the University of Notre Dame
University of Notre Dame
The University of Notre Dame du Lac is a Catholic research university located in Notre Dame, an unincorporated community north of the city of South Bend, in St. Joseph County, Indiana, United States...
. Since then many people have contributed to the project, leading to a rich set of functionality, as given below.
Library
The CDK itself is a library, instead of a user program. However, it has been integrated into various environments to make its functionality available. CDK is currently used in several applications, among which the R (programming language)R (programming language)
R is a programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians for developing statistical software, and R is widely used for statistical software development and data analysis....
, CDK-Taverna (a Taverna workbench
Taverna workbench
Taverna Workbench is an open source software tool for designing and executing workflows, created by the myGrid project and funded through the OMII-UK...
plugin), Bioclipse
Bioclipse
The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform...
, and Cinfony. Additionally, CDK extensions exist for KNIME
KNIME
KNIME, the Konstanz Information Miner, is a user friendly, coherent open source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining concept...
and Excel
Microsoft Excel
Microsoft Excel is a proprietary commercial spreadsheet application written and distributed by Microsoft for Microsoft Windows and Mac OS X. It features calculation, graphing tools, pivot tables, and a macro programming language called Visual Basic for Applications...
(excel-cdk).
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.
Chemoinformatics
- 2D diagram editingMolecule editorA molecule editor is a computer program for creating and modifying representations of chemical structures.Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical...
and generation - 3D geometry generation
- substructure search using exact structures and SMARTSSmiles arbitrary target specificationSMiles ARbitrary Target Specification is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing....
-like querieQuery languageQuery languages are computer languages used to make queries into databases and information systems.Broadly, query languages can be classified according to whether they are database query languages or information retrieval query languages...
s - QSAR descriptor calculation
- fingerprint calculation
- force fieldForce field (chemistry)In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
calculations - many chemical input/output formatsChemical file formatThis article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...
- structure generators
Bioinformatics
- protein active site detection
- cognate ligand detection
- metabolite identification
- pathway databases
General
- PythonPython (programming language)Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
wrapper - RubyRuby (programming language)Ruby is a dynamic, reflective, general-purpose object-oriented programming language that combines syntax inspired by Perl with Smalltalk-like features. Ruby originated in Japan during the mid-1990s and was first developed and designed by Yukihiro "Matz" Matsumoto...
wrapper - active user community
CDK News
CDK News is the project's newsletter and published articles between 2004 and 2007. Due to lack of a steady stream of contributions, this newsletter was put on hold.See also
- BioclipseBioclipseThe Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform...
— an Eclipse/RCP based chemo-/bioinformatics workbench - JmolJmolJmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
— Java 3D renderer (applet and application) - JOELibJOELibJOELib is a free software chemical expert system mainly used for converting chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other systems supporting...
— Java version of OpenBabelOpenBabelOpenBabel is free software, a chemical expert system mainly used for converting chemical file formats. Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, and Mac OS...
/OELibOELibOELib was an Open Source Cheminformatics library. Its actual GPLed C++ and Java successors are OpenBabel and JOELib. Its commercial successor is called OEChem.- External links :* *... - JChemPaintJChemPaintJChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems...
— Java 2D molecule editorMolecule editorA molecule editor is a computer program for creating and modifying representations of chemical structures.Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical...
(applet and application) - Blue ObeliskBlue ObeliskBlue Obelisk is an informal group of chemists who promote Open Data, Open Source, and Open Standards; it was initiated by Peter Murray-Rust and others in 2005...
External links
- CDK Project — the main homepage
- CDK Wiki — the community wiki
- CDK News — the project journal
- OpenScience.org