If you do some sort of molecular modeling, you almost certainly used one or more scripting languages to make your life easier. I’ve tried some of them and my favorite by far is Python. Other than being very readable and having simple syntax, one thing that especially makes Python very useful, is myriad of available modules that enhance the core functionality. For example you can use Numpy to do fast numerical analysis, Scipy to do linear algebra calculations, mathplolib to plot your data, MDAnalysis to analyze your simulation trajectories or use Prody to do GNM calculations.

If you are new to Python and interested to learn more about it, here are two tips:

  • If you are looking for a point to start, I recommend this interactive tutorial and learn Python the hard way.

  • There are some Python distributions available that package both core Python and useful modules in one easily installable file. Enthought Python Distribution (EPD), from Enthought, is a good one and free to academics. If you’d like to install it, go here and request an academic license and install EPD.

Have fun Pythoning!

[ Originally published here. ]