CIC Boppard 2004
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Transcript of 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