Niels and I held a JChemPaint hack-a-thon today (the IRC log). We had a quite ambitious agenda: make the renderer modular make the controller modular make a controller interface with Swing + SWT implementations All this to make the JChemPaint editor module of the CDK more easily integrate with non-Swing widget environments.

If you, like me, already upgrade to Ubuntu Gutsy, and use nxclient for remote login (highly recommended, though proprietary code), you might run into the problem that the login no longer works, returning the message “Cannot find KDE environment.”. Ubuntu’s Lauchpad (generally an excellent service) was rather uncooperative and disregarded a bug report about the problem, I found the solution with grep -ri kde /usr/NX:

I just installed XCMS 1.9.2 on my Ubuntu system. XCMS is a GPL-ed R package for metabolomics data analysis.

Clustering and classification of crystal structures is hot. Parkin hit the front cover of CrystEngComm with a story on Comparing entire crystal structures: structural genetic fingerprinting (DOI:10.1039/b704177b). Now, the story itself, while rather interesting and well written, has three major flaws:

Rich blogged about Firefly embedding MDL molfiles in PNG images , which I found really cool. Rich and Noel later showed how that metadata can be retrieved again , possibly with Python. But I did not like that Firefly could do this, and JChemPaint not. So, I started hacking. First I discovered I had to get rid of the use of JAI; then I had to adapt the JChemPaintPanel takeSnaphot() API to return a RendererImage;

An anonymous reader reported that the American Medical Association published the structure of dapagliflozin. Here are the details.

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta and wrote a script for it for chemical RDFa . At this moment, Chemical blogspace and RDF for Molecular Space (see this blog ) are using chemical RDFa to semantically markup molecular information.

Via SciFoo Planet (from Partial immortalization ) I learned about TouchGraph Google (Peter brought it into Chemical blogspace). It’s cool, though not open source. Here’s the touch graph for my blog: As you can see, plenty of blogspot bloggers around me, among which, in purple, Useful Chemistry. Funny thing is, each time I repeat the Google search, the output is different. Oh, and make sure to drag one of the halos around;

Peter wondered if data should be stored centralized or decentralized, when Deepak blogged about Freebase and Metaweb. Now, I haven’t really looked into these two projects, but the question of centralized versus decentralized is interesting. It’s MySQL versus the world wide web; it’s the PubChem compound ID versus the InChI;

Rich blogged about to Never Draw the Same Molecule Twice: Viewing Image Metadata in which he shows his molecular editor outputting images of molecular structure where the connectivity table of structure is embedded in the image. His molecular editor can read the image again, and will automatically pick up the embedded connection table. Noel showed that such can not only be done in Java, but in Python too.

I reported last week about the Molecules in Wikipedia and the plethora of templates used.