CVS commit statistics have been calculated and put online at:
Some weeks ago, Planet Blue Obelisk was setup which is a RSS feed aggregating website that gets together news from contributors to the Blue Obelisk project. Among these are CDK developers, and their feeds give more insight in CDK development.
A new open source project launched aimed at bio- and chemoinformatics: Bioclipse (at http://bioclipse.net/). CDK plugins are being built. It's in rather alpha stage but the screenshots are great!
A <a href="http://almost.cubic.uni-koeln.de/cdk/cdk_top/cdk_news/">new issue</a> of CDK News is out.
A week ago CDK5AW ended. The workshop was both rather enjoyable and exhausting. It lead to new focusses within the project and also led to a new wave of bug reports, even though a number of others were fixed during a bug squash session. Sheets of the presentations are online. Just go to the CDK website, click 'Events' -> 'CDK5AW', and there you'll find a link.
Many, many changes. Read the full <a href="http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/changelog/">changelog</a>.
We are going to celebrate CDK's fifth birthday with a CDK workshop at Cologne University Bioinformatics Center (CUBIC) from October 10-15. The most important goal of this workshop is to unite as many CDK developers and users in Cologne as possible, to socialize and have fun.
The workshop will consist discussions, presentations, a poster session, and lot's of workshops in which all can get hands on experience with using and programming with the CDK. Details can be found at
A new issue of the CDK News is out with 32 pages of interesting and diverse reading material.
A few CDK developers and users attended the International Conference on Chemical Structures 2005 in Noordwijkerhout, The Netherlands. A lot of commercial companies were present too, and the interest in open source software is growing, e.g. SciTegic's PipeLine Pilot uses open source software in some areas, for example the statistical software R. Moreover, two oral presentations referred to open source software: Steve Heller spoke about the the INChI project, and Joerg Wegner mentioned JOELib and the CDK. Additionally, one other presentation discussed research results based on software which is rumoured to be released as open source.
For about half a year a problem was known in the UniversalIsomorphismTester: finding the maximum common substructure search was not symmetric. That is, finding the MCSS given mol1 and mol2 versus mol2 and mol1 both gave the correct MCS, but often one of the two gave an additional substructure. This problem has now been solved, thanx to extensive testing and discussion with the original author.
I think this is an excellent example where users indicate problems, and the open source character of the software allows an open discussion on the problem between developers and users.
Today I've integrated Jumbo4.6 for Java1.5 in CDK CVS, so as of the next release, CDK has CML2 support on Java1.5 too.
The source code of JChemPaint is now incorporated into CDK's CVS module cdk/. This went rather painless, and three new CDK modules are now available: jchempaint, jchempaint-application and jchempaint-applet.
CVS has an improved build system. The old system intended to compile distinct modules with well defined dependencies on other CDK modules and external libraries. Not until yesterday this was fully achieved.
The online API for the CDK was still pointing to the old webpage which was removed. Now the links point to the new web server in Cologne.
Last Tuesday the CDK website was ported to a Plone system, and will be heavily updated with new content in the next weeks.
CVS has been updated with CML support. Jumbo4.6 is now supported, but only for the 1.4 JVM at this moment. I hope JVM 1.5 support for CML in CDK will follow soon.
A new issue of the CDK News is out with article on integration of CDK with R and Jmol, and the global electronic age and a new CDK website. Download it from: http://sourceforge.net/project/showfiles.php?group_id=20024
This release mostly addresses a number of build problems. If 20050116 was working for you, there is no direct need to use this version.
This release adds a 3D structure generator, more QSAR descriptors, a command-line utility to calculate QSAR descriptors, an IteratingSMILESParser, and a radial distribution function. Problems were fixed in the format detection, CML2 output, the atom type list, and SMILES generation.
The new CDK newsletter with articles about customizing file IO, NMR prediction, a 3D structure builder tool, a spectrum organizer, and more.
Jmol can be used as 3D viewer for molecular information. Details can be found on this webpage:
Because mentors.debian.net stopped providing binary debs, the repository has been moved to
After a long summer holiday period, I've found time to do a partial release: source packages + jar are now downloadable. A Unix tar.gz and Win32 package will likely follow in due time.
ChemicalMIME is a package that makes freedesktop.org compatible desktop environments, like KDE, aware of the chemical MIME types. If a chemical program, e.g. JChemPaint, then registers with this MIME type too, then such files can be opened from the internet with a web browser, like Konqueror.