chem-bla-ics

Just finished applying the latest spelling error fixes to CDK News 2.3. Took me some three hours to finish it up the 12 pages, which has mostly to the need to recompile the PDF after each change to make sure that nothing in the layout got broken.

The content contains four communications:

An Open Framework for Online QSAR Modeling

Atom types in the CDK

MQL - Development of a novel substructure query language

Stereochemistry detection in the CDK

And, ofcourse, the recurrent Editorial, FAQ and ChangeLog.

Jerome Pansanel contributed new patches for kfile_chemical; on monday actually, but I have been busy with other things, among which a presentation I have to give next monday for some 100+ analytical chemists. The patch adds support to KDE for five new chemical MIMEs: XYZ, Mol2, SMILES, VMD and GenBank. Therefore, I just released a new version (0.10), and added an announcement to Freshmeat.net.

Yesterday I had some spare time before going to a meeting about the Woordenboek Organische Chemie, so I was boldly going where no one has went before: getting the CDK module core independent of the data module. Why, you might wonder...

Well, if the as many modules of CDK become independent of the classes implementing the data interfaces, i.e. those classes that implement the org.openscience.cdk.interfaces interfaces, then it becomes possible to make alternative implementations.

A good functional molecular editor is of much important to the chemical web. There are a few small download sized editors around. JChemPaint has been available as applet for some time now, but the download size has been large. The situation has improved considerable over the past months, and the download size upon which the applet now shows up in your webbrowser is down to 538kB. A live demo is available from www.chemistry-development-kit.org.

Less then three months before the end of my contract of my PhD project. And not nearly done yet. Weekends are now spend on wrapping up bits of experimental research into something like a coherent article. And even lot's of calculations to do to answer the open questions. FreeMind is helping me organize thoughts.

Opensource chemoinformatics is a welcomed diversion now and then.

CDK News 2.3 is scheduled for this month, and origanally planned to be distributed on the CDK5AW event. So, it's a bit late. But the editorial process is converging... I realized that I forgot to mention the requirement for InChI's whenever molecules are given. So, I'm now in the process of going through the issue and add the missing identifiers...

The Jmol FAH team has just entered the Top 800 of most active Folding@Home teams. And for ExtremeOverclocking.com that's the point where they start monitoring contributions on a user level. Thus, I can now see how active I am within the team.

I've just uploaded kfile_chemical 0.9. It has new translations for ES and DA, and plugins for InChI files. It will extract the InChI string as meta data (and will thus be used by the KDE desktop search Kat), and the InChI version number.

Thinking about this, it might be useful to extract all layers as meta data, so that one can search on chemical formula and even connectivity, and find all matching structures.