The Chemistry Development Kit (CDK) is computer

software Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital comput ...

, a

library A library is a collection of Book, books, and possibly other Document, materials and Media (communication), media, that is accessible for use by its members and members of allied institutions. Libraries provide physical (hard copies) or electron ...

in the programming language

Java Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...

, for chemoinformatics and

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

. It is available for

Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

Unix Unix (, ; trademarked as UNIX) is a family of multitasking, multi-user 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, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

. It is

free and open-source software Free and open-source software (FOSS) is software available under a license that grants users the right to use, modify, and distribute the software modified or not to everyone free of charge. FOSS is an inclusive umbrella term encompassing free ...

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 Christoph Steinbeck (born 1966 in Neuwied) is a German chemist and has a professorship for analytical chemistry, cheminformatics and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia. Education Steinbeck received his PhD ...

, Egon Willighagen and Dan Gezelter, then developers of

Jmol Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the m ...

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; ; ND) is a Private university, private Catholic research university in Notre Dame, Indiana, United States. Founded in 1842 by members of the Congregation of Holy Cross, a Cathol ...

. 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 (also capitalized as JavaDoc or javadoc) is an API documentation generator for the Java programming language. Based on information in Java source code, Javadoc generates documentation formatted as HTML and other formats via extensions. ...

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

Uppsala University Uppsala University (UU) () is a public university, public research university in Uppsala, Sweden. Founded in 1477, it is the List of universities in Sweden, oldest university in Sweden and the Nordic countries still in operation. Initially fou ...

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

KNIME KNIME (), the Konstanz Information Miner, is a data analytics, reporting and integrating platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" con ...

) and for Excel, 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 notable 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 ...

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

query language A query language, also known as data query language or database query language (DQL), is a computer language used to make queries in databases and information systems. In database systems, query languages rely on strict theory to retrieve informa ...

* 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 for 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 Simplification, Simplify, or Simplified may refer to: Mathematics Simplification is the process of replacing a expression (mathematics), mathematical expression by an equivalent one that is simpler (usually shorter), according to a well-founded or ...

(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 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 sapph ...

wrapper * active

user community A virtual community is a social network of individuals who connect through specific social media, potentially crossing geographical and political boundaries in order to pursue mutual interests or goals. Some of the most pervasive virtual commu ...

References

External links

*
CDK Wiki
– the community wiki
Planet CDK
- a blog planet

OpenScience.org
{{Chemistry software Bioinformatics software Chemistry software for Linux Computational chemistry software Free chemistry software Free software programmed in Java (programming language)