In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The Groovy Cheminformatics with the Chemistry Development Kit book is a project that has run since 2009.

Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.

The data classes of the Chemistry Development Kit are mutable, unlike those of Octet. This means that other classes may need to respond when the content updates. For example, a render class. CDK’s ChemObject provides a notifyChanged() and addListener() methods for this.

An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.

OpenSource, OpenData and OpenStandards are not as strong in chemoinformatics as they are in bioinformatcs, where it is common knowledge that sharing is a good. Today, the JCIM published on the web an article about the Blue Obelisk movement, which promotes these three idealogies. Several open source projects participate, amongst which the CDK, Jmol, JOELib, OpenBabel, Chemical Markup Language, Bioclipse and Kalzium.

Gemma Holiday’s article on CMLReact was published in the january issue of the JCIM (doi:10.1021/ci0502698), which seems to be marked as sample issue right now. She used CMLReact as data format for MACiE (see doi:10.1093/bioinformatics/bti693), a database of 100 enzyme reactions, with fully annotated reaction mechanisms, making this an remarkable and insightfull database.

This weekend I continued my work on getting the CDK and Jmol run with free, open source JVMs. Really, a lot works fine, as reported earlier in this blog: JChemPaint works and Jmol almost works (see the Classpath’s FreeSwingTestApps wiki page), and well over 95% of the CDK JUnit tests run without trouble too. So it comes down to identifying what does not run properly, and file bugs for this. For example, 26101 and 26108.

Because I am still looking forward to testing CDK against the latest Classpath 0.20, I downloaded cacao 0.94-1 for Debian sid, then tried to compile CDK with it: JAVA_HOME=/usr/lib/jvm/cacao ant -Dbuild.compiler=gcj clean test-all But that hangs at some point with zero load. I have no idea what is going on there.

Free at last! Well, not quite yet, but close enough anyway: my PhD contract has ended; last friday was my last working day, which my collegues and I celebrated with a visit to Nijmegen oldest bar, In de Blauwe Hand . But I still have my manuscript to finish. This formally ends a period of almost 12.5 years at the Radboud University Nijmegen. Starting last monday I’m at home, trying to get things finished as soon as possible.