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 readme.md of GitHub is not straightforward the first time round. Hence, I wrote this simple guide to doing so.

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!

RDKit for Rosetta: PLP ligand space as an example

Docking requires a molecule to dock. Preparing a ligand is often tricky, especially if the ligand is complicated, such as PLP. PLP is an interesting cofactor as it catalyses the reaction while the protein chooses the ligand. It binds tightly to the active site via its phosphate and its pyridine ring, while the metabolite to be transformed forms a Schiff base with it. Therefore, one would think that it makes easy to explore chemistry space with it. However, several technical hurdles are encountered, making it quite didactic.

Toasty CSS with BS4

In Bootstrap 4 you can have appear small alert-like rectangles, called toasts. However, getting these to work like notifications on top of the page in the top right is not trivial as it requires some CSS trickery. Here is what is required.

Pictograms with Plotly and FontAwesome

Plotly is one of the most powerful graphing packages for Python, JS and Julia. The cool feature is that the graphs are HTML bases with interactive graphs as opposed to a static jpg. There are several graphs that are missing, one of which is a pictogram. It's not a very silly graph, but  Luckily a pictogram is easy-ish to make.

PDB numbering rollercoaster

The position in a crystal structure and the protein sequence rarely match. In fact, there are four parts of start-end:

• position in whole protein,
• position in extracted sequence,
• position in residues stated in the PDB/mmCIF structure and 
• position which actually has coordinates.

Jupyter notebook progressbar

I have this rather handy wee piece of code I'd like to share: a Jupyter notebook Progress bar.