Oliver Beckstein

I don't think that we need to add the molecular structure next to the solvation plots unless you want to highlight specific atoms. Otherwise I'd expect a molecular structure to...

Each atom should only be counted once. There's a single closest interaction between a solvent atom and the solute (barring coincidental equidistant triangles).

@cadeduckworth is this something you'd want to complete for a MDPOW paper? Can you resolve the conflicts so that one can look at the changes in the context of the...

Instead of shipping the yml file with the docs, we should link it to the raw file on GitHub under the appropriate release tag, eg https://github.com/Becksteinlab/MDPOW/raw/release-0.8.0/doc/examples/benzene.yml (and the file in...

This might need a rewrite of EnsembleAnalysis to directly use a full analysis over a Universe. If so, first raise a separate issue for those changes to the framework and...

Have you figured out how much work it is going to be to add h-bond analysis?

@cadeduckworth here's the issue for adding H-bond analysis, in case you want to have a go. Perhaps @ALescoulie could help with reviewing once you get a PR up?

You should not need to do two runs. If you define donors and acceptors appropriately then you should only need one run and then you can sort the resulting list...

Also HydrogenBondAnalysis has the `between=[group1, group2]` keyword to only look for inter-group H-bonds https://userguide.mdanalysis.org/stable/examples/analysis/hydrogen_bonds/hbonds-selections.html#Hydrogen-bonds-between-specific-groups See also tutorial in https://userguide.mdanalysis.org/stable/examples/analysis/hydrogen_bonds/hbonds.html

See also #194 — remove bundled tempdir whenever you come across it...