Today I received news on the Jmol user list that Lubert Stryer’s Biochemistry replaced the proprietary Chime with the open source Jmol. The third edition from which I learned biochemistry in my first year at the university did not feature a CD with live figures, but I am very thrilled to see a program on which I have actively programmed hit a text book I used myself in the past.
About two years ago a student started with me to work on the use of 1D NMR and IR spectra in quantitative structure-activity relationship (QSAR) work, with the goal to show that these spectra contain 3D information relevent to QSAR models. It is known that these spectra depend on the 3D conformation of the molecule.
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.
This is the best news I heard in weeks! The US Patent and Trade Offfice spoke with open source representatives about ways to deal with open source software as prior art. Apparently, their problem was how to be sure about release dates of open source, and authoritative sites like SourceForge.net, FreshMeat.net help a lot here, which extensive logging of releases.
While waiting for a Dragon calculation to finish (it does not work for molecules with more than 300 atoms!), I updated CDK’s build.xml to support gjdoc. The build script is now able to compile the custom doclets we use for creating the src/*.javafiles and others from the Java source files. And using gij I could also run CDK’s 1688 JUnit tests!
One of the things I had not fully figured out up to today, was how to configure my Kubuntu system to easily view DVDs on our TV, using my NVIDIA’s TV-OUT. I’ve seen xorg.conf files that define a X11 server for the monitor and a second for the TV, and files that use TwinView. Now, I did not really like the way first option worked, so tried the second.
Derek Lowe is the author of the blog In the Pipeline which is really fun to read. Derek works in pharmaceutical industry and gives a great insight in how things work in that field of molecular sciences. Yesterday he blogged about What Makes an Ugly Molecule? , and touches the Rule-of-Five, the hydrochloric acid bath (aka stomach), and other reasons that make molecules ugly.
After the three obligatory days of christmas holidays (fun, especially with two children, but very exhausting), it is time to get back to business again. I’m still at my father-in-laws place with only XP installed, so booted the Knoppix 4.0.2 DVD I burned last friday. Eclipse is not working, but being able to use Kmail to read my email again is just what you need as in internet-junkie.
In a recent JCIM article, Schuffenhauer compares a few subset selection methods, and notes that some of them reduce the average complexity of the molecules. They put this in relation to other research that states that lead compounds with high complexity have higher activities. Recommended reading material for the holidays.
One of the Classpath developers pointed me to their CVS statistics when I asked them how actively their project is currently developed, i.e. the number of active developers. The pages are generated with StatCVS, and I ran it one the CDK too. I knew I did a lot of work on the CDK, but never realized that 62.7% of the commits were mine! Keep in mind, though, that a lot of these commits are for code maintainance!