R News special issue on chemistry

R News just released a special issue on the use of the versatile statistics program R in chemistry. It features six articles amongst which one by Rajarshi Guha on the CDK-R bridge, and one by my supervisor and me on the use of self-organizing maps to cluster crystal structures. less than 1 minute read

Chemical blogspace

We all know chemical space; Chemical blogspace (Cb) is different: it is the chemistry discussed in blogspace. Cb is build on the opensource software of Postgenomic.com which I bloged on before . The now running Cb aggregates 19 blogs and, like the original, extracts linked (cited or reviewed) articles from literature. less than 1 minute read

Bioclipse gets a new extension point

I hacked in a new extension point for Bioclipse yesterday, based on a proposal I made earlier. The new extension point (EP) is called ChildResourceCreator and allows creating child resources for a given IBioResource. One application where this is very useful is the CMLRSS application (earlier blog ), or any RSS or Atom enriched with any other XML language. Here, child resources are created for each feed entry resource with as content the foreign XML, e.g. the CML bits in the blog. 1 minute read

CML Explained

Recently, a new generation of Chemical Markup Language CML users seem to hit the learning-curve-wall; there seems to be a niche in explaining the use of CML, so here goes. My new (third) blog will discuss frequently and less frequently asked questions about the use of CML. less than 1 minute read

Small java applet for 2D structure drawing

Trepalin et al. published in Molecules the article A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL) (open access PDF). The applet is about 250kB (though the article mentions 200kB) in size and downloadable from the MCDL project on SourceForge (license: Public Domain). The article compares the applet with the JChemPaint applet and notes that their applet is much smaller. Both allow a template database for automated structure diagram generation, and the database that comes with the MCDL applet contains 105 fragments, whereas the JChemPaint applet contains a few. less than 1 minute read

Classpath 0.92 has been released

Bling! Bling!. Mark Wielaard announced the GNU Classpath 0.92 release, with the following changes: an alternative awt peer implementation based on Escher that uses the X protocol directly. Various ImageIO providers for png, gif and bmp images. Support for reading and writing midi files and reading .au and .wav files have been added. Various tools and support classes have been added for jar, native2ascii, serialver, keytool, jarsigner. A GConf based util.peers backend has been added. Support for using alternative root certificate authorities with the security and crypto packages. Start of javax.management and runtime lang.managment runtime support. NIO channels now support scatter-gather operations. less than 1 minute read

Fortran and XML: FoX reads and writes CML

Mix one of the oldest and one of the latest computer technologies, and you get FoX (BSD license), a Fortran library for reading and writing Chemical Markup Language, and thus XML. Amazing, what Toby White achieved, though he did not start from scratch: “FoX evolved from the initial codebase of xmlf90, which was written largely by Alberto Garcia and Jon Wakelin.” (source: cml-discuss mailing list). less than 1 minute read