One of the things I like most from being a computational chemist, is the possibility to automate tasks by using scripts.
There is usually no problem for automating almost anything, but unfortunately, there are a few tricky to automate tasks, for example, when it comes to generate atomic/molecular figures.
Let’s think that we have to calculate the energies of a lot of different molecules, and after doing that, we certainly need to check the results. We can easily “grep” the total energy (or any other numerical/ASCII value) from the output files but usually, the only way to take a look to the geometry of the structures is by going trough all the outputs and opening them with a graphic molecular viewing program (such as molden, vmd, xmakemol, jmol, …). This task can be quite painful, specially for the geek people who does not like wasting their energy using the mouse if it is not completely necessary. Continue reading →