Sunday 19 June 2022

Top 10 silliest PDB residue names for ligands!

UPDATE: The PDB will finish 3 letter chemical component IDs sometime before 2024 at which point they will switch to 5 letter codes, which will be usable solely in CIF format:

In some situations it is handy to use in an in silico experiment a 3-letter residue name that is not taken in the PDB. For example, PyRosetta has a system of pregenerated topologies for PDB components, which can cause issues when a ligand is loaded and the movers may use that over an incorrectly provided residue type / param file, resulting in a blown up mishapen ligand —an overly common incident*. As a result, having a list handy of what is taken is helpful. Herein are some silly observations about what the taken and untaken names are —but not ranked as a top 10, because this is not a science blog, not my local newspaper.

Saturday 4 June 2022

Annotate as you go

There's a counter-constructive saying: a project is dead as soon as you add documentation (Aeschylus, I believe).

This could not be more incorrect. Whereas it is true that writing documentation on an evolving project will quickly result in the fresh documentation becoming quickly invalid, it is a planning truth that writing documentation once a project is finishing is impossible because there are a hundread and one more pressing issues. Therefore, adding docstrings to each function, method and class in Python as one goes along is by far more advantageous. Once this is done, however this information needs to be transmuted into documentation. Here is how once can set up ReadTheDocs without falling into a few traps, as the documentation generator Sphinx is ironically weirdly documented and should be done ideally early on, so one knows what mistakes one's making.