MDAnalysis project

This page contains the details of a technical writing project accepted for Season of Docs.

Project summary

Open source organization:
MDAnalysis
Technical writer:
lilyminium
Project name:
A user guide structured by topic
Project length:
Long running (5 months)

Project description

A guide to the MDAnalysis library, separate from the API reference, that includes:

  1. A detailed guide to the data structures used in MDAnalysis. This page will introduce the Atom, AtomGroup, and Universe classes; include I/O options; and contain information on manipulating Atoms and combining AtomGroups.

  2. A page on the Analysis building blocks. The AnalysisBase class, AnalysisFromFunction class, and analysis_class functions form the basis of any user-defined analysis. What each class does under the hood is worthwhile knowing, e.g. if it’s analogous to numpy.vectorize.

  3. A page on selecting groups of atoms using Universe.select_atoms. Both the technical details and the molecular dynamics knowledge behind the way that this is implemented.

  4. A page on topologies. Users should understand the data structure, usage, manipulation and framework for building systems.

  5. A page on available visualization methods, both for the trajectory and for current analyses that return data for visualization.