cic boppard 2004

The Chemistry Development KitAn OpenSource Java library for structural

chemo- and bioinformatics

Egon Willighagen, Radboud University NijmegenChristoph Steinbeck, Cologne University BioInformatics Center

18. CIC-Workshop14.-16. November 2004, Boppard

The Chemistry Development Kit?

Library of Standard Algorithms● Reduce need to rewrite code● ChemoInformatics education

Toolkit for prototyping● 2D/3D rendering● file IO

Java● Object oriented● Portability● Applet (and Internet technologies in general)● ... speed ?

Molinformatics● IO (CML, MDL, PDB, INChI, ...)● SMILES parsing and canonical generation● Isomorphism checking● Substructure search (and SMARTS)● Maximal Common Subgraph Searches● Gasteiger charges● Ring searching (SSSR)● Structure Diagram Generation● 2D Rendering (and 3D via Jmol)● Fingerprinting● HOSE codes● Atom typing

Standard Algorithms

Simple example

3D Rendering: Jmol

Rendering Features● wireframe/ball-sticks/etc● protein

● cartoon● backbone

Rasmol Scripting

Applet and Application

History of the Project

September 2000the CDK emerged from the CompChem libraries used by Jmol, JChemPaint and Seneca.

February 2001the CDK project registered at SourceForge.net

March 2003

Steinbeck, C. and Han, Y. and Kuhn, S, and Horlacher, O. and Luttmann, E. and Willighagen, E. J.Chem.Inf.Comput.Sci. 2003, 43:493-500

July 2004first release of CDK News

CDK Community

Active development● 10 active and 30 part-time● highly internal

Users● 50+ users on user list● many projects using the library

Communication● Email: user list, developers list● Internet Relay Chat● Informal meetings● CDK News

CDK News

Newsletter (ISSN 1614/7553)● With articles on the use of CDK● ChangeLog / Literature / FAQ● Free, print copies available

Vol. 1 Issue 2● Customizing file IO● First steps in the implementation of a force field● Spok - The Spectrum Organisation Kit● Predictor● Konqueror web shortcuts to the CDK API

A few applications...

Chemistry● NMRShiftDB● 2D diagram editor (JChemPaint)● Seneca (structure elucidation)● CML Rich Site Summary● Nomen (IUPAC name parser)

Bioinformatics● Brenda (enzyme database)● Pathway analysis● Enzyme reaction mechanisms

Many more...● A few commercial software programs● Some project in development

NMRShiftDB

C. Steinbeck, S. Kunh et al. J.Chem.Inf.Comp.Sci., 2003, 43:1733-1739

P. Murray-Rust, H.S. Rzepa, M.J. Williamson, and E.L. Willighagen, J.Chem.Inf.Comp.Sci., 2004, 44:462 - 469

Chemistry enhancedRich Site Summary (CMLRSS)

Enzyme reaction Mechanisms

➔ Large library with key algorithms

➔ Active developer and user community

➔ Has been used in several projects

New areas of interest● Descriptor calculation (QSAR)● Structure optimization (force field)

Summary

Code contributions from:

Ulrich Bauer, Fabian Dortu, Dan Gezelter, Rajarshi Guha, Yonquan Han, Kai Hartmann, Christian Hoppe, Oliver Horlacher, Miguel Howard, Geert Josten, Anatoli Krassavine, Stefan Kuhn, Daniel Leidert, Edgar Luttmann, Nathanaël Mazuir, Stephan Michels, Peter Murray-Rust, Chris Pudney, Jonathan Rienstra-Kiracofe, David Robinson, Bhupinder Sandhu, Jean-Sebastien Senecal, Sulev Sild, Bradley Smith, Christoph Steinbeck, Stephan Tomkinson, Joerg Wegner, Stephane Werner, Egon Willighagen, Yong Zhang.

Acknowledgments