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Evidence of Aromaticity
I have been working on a new atom type perception engine for the CDK, after having decided that the existing atom type lists where not sufficient for the algorithms we have in the CDK. The new list is growing in size, and basically contains four properties (besides element and formal charge):
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Glueing BioMoby services together with JavaScript in Bioclipse
Ola has been doing a good job of integrating BioMoby support into Bioclipse. Earlier he completed a GUI for running BioMOBY services, and added more recently a JavaScript wrapper too, using the Rhino plugin developed by Johannes.
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BioSpider: another molecule search engine
I just ran into BioSpider. Unlike ChemSpider, BioSpider crawls the internet (well, this list of sources really) to find information, and depending on what it finds it continues the search. Below is a screenshot of an intermediate point after starting with the InChI of methane:
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One Billion Biochemical RDF Triples!
That must be a record! Eric Jain wrote on public-semweb-lifesci:
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My blog turned 2
A bit over two years I posted my first blog item, Chem-bla-ics, introducing the topic of my blog. In January this year I explained why I like blogging.
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Bob improved the POV-Ray export of Jmol
Bob has set up a new interface between the data model and the Jmol renderer, which allows him to define other types of export too. One of this is a POV-Ray export, which allows creating of high quality images for paper. Jmol has had POV-Ray export for a long time now, but never included the secondary structures or other more recent visual featues. PyMOL is well-known for its POV-Ray feature, and often used to create publication quality protein prints. The script command to create a POV-Ray input file takes the output image size as parameters:
