SMILES has a convenient feature to mark elements from the organic subset in lower case, indicating a particular hybridization state (aromaticity). The locations of double bonds are then not explicitly given, reflecting the delocalized nature of those systems:

However, there are many situations where you do like to know the position of those double bonds, or at least on solution of the set of possible combinations, such as:

Finding the positions of the double bonds is one of the core algorithms in cheminformatics.

This is what hackathons are about: sitting in the same room, hacking new stuff, to boldly go where no one has gone before. Who knows where you end up. This morning, I hacked up a SBML plugin for Bioclipse.  OK, it is not yet showing a nice diagram, but not bad for two hours of hacking.

Some six weeks after the 1.4.9 release, and not including the recent work by Kevin and Klas on improving (which you can test here), here's the next stable CDK release.

The first thing you'll notice is the long list of patches. This is primarily caused by the inclusion of the renderextra module from the CDK-JChemPaint patch, by Arvid, Stefan, Gilleain, Niels, and me. This part of the rendering engine brings in more rendering functionality. The controller code for editing is still excluded.

In reply to a question on the CDK user mailing list, I wrote up for my CDK API book how to define custom descriptors (nitrogenCount and oxygenCount) using the parameter approach:

The Java code is a bit more complex, requiring more Java language specific code. But the key is simply to use the the setParameters() method.
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I just ran into this interesting post on the R-bloggers Planet. The described R functionality allows you to compile R code (to byte code) so that it will no longer be interpreted but actually run. That is a performance boost. I guess in due time we will see R use JIT technologies, so that the difference will disappear, but for now, a good thing to know about.
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Google introduced a cool new translate widget for Blogger.
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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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