LaserJock

I’ve been involved a little bit with the Avogadro project. Avogadro is a cross-platform 3D molecular editor. It’s written in C++/Qt4 for people who care and sports a new Python console for people like me who want to have our cake and it it too. Here are the things I like about it:

• cross-platform – my lab has both Linux and OS X machines. Being able to use the same application on all of them is a big plus
• auto-optimization – you can turn on an autooptimizer that does does geometry optimizations on the fly as you move atoms around. Not only does this look awesome, it’s also a great teaching tool.
• Gaussian input – we have an undergrad this summer in our lab and he’s working on some MO calculations using Gaussian. The Avogadro Gaussian input tool was really easy to having start using and he didn’t have to spend time figuring out all the syntax/options.

For a project this young, it’s really coming along nicely.

Anybody who knows me knows that I’m not a programmer, I don’t even play one on TV .  I’m a PhD Physical Chemistry student and an experimentalist at that. I knew nothing about distro or software development for most of the time I’ve used Linux. A little over a year ago I figured out how to get on freenode hopped on #ubuntu-motu . I was sucked into the MOTU world and have been known as a raging Ubuntu-holic MOTU.  So now that I’ve experienced a little distro development I’ve been itching a little to do some software development.  Well, the short story is through a series of events I found Gnome Chemisty Utils (and it’s author Jean Bréfort) and a group of chemists interested in open standards and open source in the area of chemoinformatics called Blue Obelisk. Now, putting this all together I ended up learning a little C++ and GTK to create a new color scheme for the gchemutils periodic table app that reads in data from the Blue Obelisk Data Repository (BODR). The new scheme “colorizes” the elements by family (noble gases, alkali metals, etc. ). The fruit of my labor, released today as a part of Gnome Chemistry Utils version 0.7.4, is shown in the following screenshot:

So if you happen to be interested in periodic tables (you know you are) then grab BODR 4 and gchemutils 0.7.4 and have fun.

Next step: figure out how to get all this fun stuff in Universe for Feisty!