The Chemistry Development Kit (CDK) is computer

software Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work. ...

, a

library A library is a collection of materials, books or media that are accessible for use and not just for display purposes. A library provides physical (hard copies) or digital access (soft copies) materials, and may be a physical location or a vi ...

in the programming language

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mo ...

, for chemoinformatics and

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...

. It is available for

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for ...

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which i ...

Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, a ...

, and

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of ...

. It is

free and open-source software Free and open-source software (FOSS) is a term used to refer to groups of software consisting of both free software and open-source software where anyone is freely licensed to use, copy, study, and change the software in any way, and the source ...

distributed under the

GNU Lesser General Public License The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate a software component released under the LGPL into their own ...

(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 University of Notre Dame du Lac, known simply as Notre Dame ( ) or ND, is a private Catholic university, Catholic research university in Notre Dame, Indiana, outside the city of South Bend, Indiana, South Bend. French priest Edward Sorin fo ...

. The first source code release was made on 11 May 2011. Since then more than 100 people have contributed to the project, 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. Due to an unsteady rate of contributions, the newsletter was put on hold. Later, unit testing, code quality checking, and

Javadoc Javadoc (originally cased JavaDoc) is a documentation generator created by Sun Microsystems for the Java language (now owned by Oracle Corporation) for generating API documentation in HTML format from Java source code. The HTML format is used ...

validation was introduced. Rajarshi Guha developed a nightly build system, named Nightly, which is still operating at

Uppsala University Uppsala University ( sv, Uppsala universitet) is a public research university in Uppsala, Sweden. Founded in 1477, it is the oldest university in Sweden and the Nordic countries still in operation. The university rose to significance durin ...

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

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, CDK-Taverna (a

Taverna workbench Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name ''Taverna Workbench'', then a project under the Apache incubator. Taverna allowed users to integrate many ...

plugin),

Bioclipse The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009, and a command line version in 2021. Like any RCP applic ...

, PaDEL, and Cinfony. Also, CDK extensions exist for Konstanz Information Miner (

KNIME KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks ...

) and for

Excel ExCeL London (an abbreviation for Exhibition Centre London) is an exhibition centre, international convention centre and former hospital in the Custom House area of Newham, East London. It is situated on a site on the northern quay of the ...

, called LICSS

. 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.

Major features

Chemoinformatics

* 2D

molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ...

and generator * 3D geometry generation * ring finding * substructure search using exact structures and Smiles arbitrary target specification (SMARTS) like

query language Query languages, data query languages or database query languages (DQL) are computer languages used to make queries in databases and information systems. A well known example is the Structured Query Language (SQL). Types Broadly, query language ...

* QSAR descriptor calculation * fingerprint calculation, including the ECFP and FCFP fingerprints * force field calculations * many input-output

chemical file format A chemical file format is a type of data file which is used specifically to depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files ...

s, including

simplified molecular-input line-entry system The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors ...

(SMILES), Chemical Markup Language (CML), and chemical table file (MDL) * structure generators * International Chemical Identifier support, via JNI-InChI

Bioinformatics

* protein active site detection * cognate ligand detection * metabolite identification * pathway databases * 2D and 3D protein descriptors

General

* Python wrapper; see Cinfony *

Ruby A ruby is a pinkish red to blood-red colored gemstone, a variety of the mineral corundum (aluminium oxide). Ruby is one of the most popular traditional jewelry gems and is very durable. Other varieties of gem-quality corundum are called sapp ...

wrapper * active user community

History

Library

Major features

Chemoinformatics

Bioinformatics

General

See also

References

External links