Saturday, 30 November 2019

Convert Python docstrings to GitHub markdown readmes

The Greek philosopher Epictetus said that a day reverse engineering a piece of code saves you half an hour reading the documentation. A maxim still valid to this day. Nevertheless, documenting code is important. With PyCharm and the push towards typehinting in Python writing docstrings is fairly simple. However, getting docstrings into the of GitHub is not straightforward the first time round. Hence, I wrote this simple guide to doing so.
Do note that for medium/big projects, using ReadTheDocs is recommended over this hack: ee the guide to setting up Sphinx for ReadTheDocs

Thursday, 7 November 2019

Go away glycerol!!

Due to the nature of crystallisation additives are often found in PDB structures. These are generally unwelcome, especially if you want to extract ligands. In fact, I have heard only once someone talk excitedly about their crystallisation reagent in their structure, but only because they were trying to flog it off as an allosteric binding site. Generally, they are just annoying. Luckily you don't need reinvent the wheel as a list or two already exist!