Resources

Below is a list of useful prior art. These might get included (in some form or another) in the User Guide that is being created.

Collections

List of useful general resources:

• https://github.com/MDAnalysis/WorkshopHackathon2018
  • Workshop delivered in 2018. Has various notebooks that people went through. Has lots of code examples and highlights things that we felt were unintuitive and needed highlighting.
• https://github.com/Becksteinlab/MDAnalysis-workshop
  • Workshop given in 2015. Was used as the basis for the 2018 materials, but might have diverged.
• https://github.com/MDAnalysis/MDAnalysisCookbook
  • A lot of scripts and examples.
  • Mostly outdated.
• https://github.com/MDAnalysis/binder-notebook
  • reasonably up-to-date executable notebooks with code examples
  • sometimes ahead of the published release...
  • see the binder-notebook/issues for "wished-for" examples
• MDAnalysis FAQ — started recently, not comprehensive. Maybe turn into its own repo + published docs or add to the UserGuide?

Individual examples

More specific examples:

• https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/notebooks/eth_hbonds.ipynb
  • A tutorial on manually finding hydrogen bonds in ethanol. Was written to try and show how the distance calculation building blocks come together.
• https://gist.github.com/richardjgowers/b16b871259451e85af0bd2907d30de91
  • Doing an equivalent of editconf to multiply/tile out a single Universe
• https://gist.github.com/richardjgowers/85a652e61690143b04d35acbac1fa2b5
  • Adding arbitrary attributes to a MDAnalysis Universe
• https://gist.github.com/richardjgowers/d9cf9246db98cf298b606852742009c2
  • Similar to previous, shows how to tag atoms as belonging to a "Layer", then also being able to select these via select_atoms