Day 5 was formally the last day (see also the summaries of day 1 , day 2 and day 3/4 ) of the Chemistry Development Kit Bug Squash Party (BSP). Miguel uploaded the last bits of his CDK PDBPolymer to CML to CDK PDBPolymer roundtripping functionality (closing a bug and a feature request in one go). Have not tested this first hand yet, but looking forward to playing with this bit of code.
Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2 ). But here it is. Day 3 Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit.
Like yesterday I will give short overview of things done at the Chemistry Development Kit Bug Squash Party (BSP). I think Stefan was the only to fix and close a bug report yesterday.
I plan to do a daily coverage of the Chemistry Development Kit Bug Squash Party (BSP). While Stefan was working hard to get the wiki machine back online after a hard-disc crash, Rajarshi, Miguel and me have been working hard. Miguel started to work on missing JUnit tests for bugs reported on SourceForge and Rajarshi fixed PMD, JavaDoc and other problems.
There are a number of links I wanted to blog about, but never really had time for yet. Here’s a short review of a them. Bio::Blogs is a series of summary/review articles of bio related blogs, and definately worth putting in your aggregator. Maybe someone is interested in setting up a Chemo::Blogs for chemistry blogs? My del.icio.us (social bookmarking) network informed me about HTML Slidy, an XHTML based PowerPoint replacement.
Some time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information. Using the new extension point, Bioclipse now treats PDB files as complex documents, creating child resources for the 3D molecular model (using the CDK plugin), and a sequence resource (using the BioJava plugin).
Bernard Munos at Eli Lilly & Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&D reinvigorate drug research?
Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse . Oscar3, however, is capable of more than the name2structure of OPSIN (see also 10.1039/b411033a;
Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms.
ケムインフォマティクスに虚空投げ runs a story on how to calculate geometrical properties of a 3D structure using CDK’s ForceFieldTools. This class contains a few methods to calculate distances between atoms and angles between bonds. This tools class is special as it uses vecmath GVector objects, which just contain atomic coordinates, likely suitable for extensive computation, as expected in CDK’s force field implementation.
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.
