After some difficulties this week with making an export of CDK plugins in the Bioclipse2 Cheminformatics feature of with the cdk-eclipse software, I got the following cute Bioclipse2 script up and running:dimethylether = cdk.fromSMILES( "COC" );

cdk.addExplicitHydrogens( dimethylether );

cdk.generate3dCoordinates( dimethylether );

// save as CML

cdk.saveCML( dimethylether, "/Virtual/dimethylether.cml" );

ui.open( "/Virtual/dimethylether.cml" ); // this should open a JmolEditor

jmol.minimize(); You can see four of my favorite cheminformatics tools integrated: CDK is used to convert a SMILES into connection table with add explicit hydrogens, and to create initial 3D coordinates (with the code from Christian Hoppe, and thanx to Stefan for fixing that code in the CDK 1.1.x branch!).

Recently, I have been blogging about Git:GitToDo support for FreemindGit mirror for the CDKCDK development with branches using GitOffline CDK development using git-svn One concern expressed by people was the lack of integration with IDEs. Now, an Eclipse plugin seems well on its way:

With a experimental update site (http://www.jgit.org/update-site), the plugin is just an Eclipse reboot away.

A new environment means new tools. Bioclipse is Eclipse RCP-based, so colleagues work with Eclipse and are much more into Eclipse too. For example, into Mylyn. Mylyn is a tool to track tasks and assign context to them. The tasks I am interested in (for this blog item), is fixing bug reports. Mylyn is rather suited for this, as it allows linking Java source files to bug reports. With a growing list of projects in my navigator, browsing them becomes difficult because the list is way too long.

About a week ago, I hooked up my GitToDo software with Freemind. This allows me to organize the projects I am working on, without having to code this in GitToDo directly.

As you might have seen, we, Uppala and the EBI, are working on the next generation JChemPaint. JChemPaint is an editor, and therefore, consists of a mode (IChemModel), a view (IRenderer) and a controller (IController). See the many posts in Gilleain's blog.

For the renderer I have set up a wiki page which I'll be hacking in the next days, which shows how a IChemObject content should be rendered in JChemPaint.

Five days ago, my chem-bla-ics blog turned 3. Here's the first post. It defined:chemblaics is the application of open source software in cheminformatics, chemometrics, proteochemometrics, etc, making experimental results reproducable and validatable. Much has changed to the field since that post, for the better of chemical sciences.

Some time ago Noel ran a poll on chemoinformatics and cheminformatics, so I set up a poll too in part #1 of this series. The outcome is clear:

The Obernai meeting strongly suggested chemoinformatics [1], but the start of the open access Journal of Cheminformatics is the killer. I can no longer resist: I'll follow the wish from my advisory board, and the general trend around the world (except India).

Just updated Bioclipse2 with Jmol 11.6 RC 18:

Now working in Uppsala makes Bioclipse my default life sciences platform, and I'll be porting older Bioclipse1 plugins to Bioclipse2, which has a much better architecture.

Bioclipse2 does not have a native Jmol Console, but script commands can easily be run with jmol.run() (written by Jonathan). I wonder if it would be hard to have a JmolScript view like this JavaScript Console...
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Lee et al. published last week a paper on pKa prediction (doi:10.1021/ci8001815). As the paper says, the pKa, and in particular the ionic state of a molecule at physiological pH, affects pharmacokinetics and pharmacodynamics. The paper describes a (binary) decision tree using presence or absence of SMARTS substructures to traverse the tree, allowing prediction of monoprotic molecules.

Now, the paper's Supplementary Information contains the full model.
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There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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