chem-bla-ics

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.

But there are many other interesting posts, and, something that my blog still lacks, comments by many users, discussing the ideas he posts, making his blog even nicer.

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. A computer is just not complete without a nice KDE session hanging around.

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, so 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! Next in line are steinbeck and rajarshi.

For some weeks now I have been thinking about bug 1309731 : "ModelBuilder3D overwrites Atom IDs". The ModelBuilder3D is a complex piece of source code, reusing many other parts of the CDK, including atom type perception.

Somewhere in October, however, I found that Taverna could not create 3D models and convert these into reasonable CML because the Atom ID's were messed up.

I drop in on the #classpath channel of freenode.net IRC network, where the #cdk channel runs too. The #classpath channel is for the Classpath project which is developing the free Java libraries used by most open source virtual machines.

A Slashdot.org item was mentioned "Java Is So 90s". It lead to a funny discussion about what that would make C/C++ and Fortran.

I reported earlier that the CDK has been updated in CVS to use CML from the new Jumbo 5.0. The transition actually involved a lot of changes in the CDK, some I would like to address in the following comments. One thing is that CML write support (not reading!) uses the new Jumbo library which requires Java 1.5. Thus, if Java 1.5 is not available, then CML writing should not be compiled. This is how this is done.

The JavaDoc

The CDK makes extensive use of JavaDoc taglets.

Tobias commited Jumbo 5.0 to CDK CVS, so that the CDK is now again up to date with the latest CML library. Note that Jumbo 5.0 requires Java 5.0.

At first all JUnit tests seems to work, but apparently the CML2Writer tests were skipped because they were only run when Java 1.4 was found. I updated the test for the a appropriate Java version, and then it turned out that most tests fail. So those running CDK from CVS and depent on CML writing: hang on, it will be fixed very soon.

The code clean up after CDK's interfaces transition is in progress, and two CDK modules are now independent of the data module. After doing the core module, the standard was next, and I finished this yesterday. The dependencies in CVS now look like (click it to get a larger view):

This UML diagram was made with , and the source is in XMI in CVS.

After requests I added yesterday more visible the RSS and Atom feeds for the Planet Blue Obelisk. They are linked in the menu on the right, and as alternative links to the document. These should show up in most recent webbrowsers as feed icon in the lower right corner of the browser window. It is often an orange icon. I also added a 'Leave a comment' link to encourage people to leave comments on items.