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MDAnalysis / waterdynamics

Analysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
https://mdanalysis.org/waterdynamics
GNU General Public License v2.0
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rewrite waterdynamics to use AnalysisBase #18

Open orbeckst opened 1 year ago

orbeckst commented 1 year ago

Is your feature request related to a problem?

Code in analysis.waterdynamics does not behave like most of the analysis tools that ship with MDAnalysis.

There are various inconsistencies, notably

and the current approach also does not allow us to easily parallelize (#4080 ).

Describe the solution you'd like

Refactor code to use AnalysisBase, see how to write your own analysis code

Describe alternatives you've considered

Do nothing and maintain the code as is (but do not consider any enhancements or improvements).

Additional context

We are also considering decided moving wateranalysis to a separate MDAKit. Once the code is on a separate development track, it may be easier for users/developers to contribute.

MDAnalysis/mdanalysis#4310

orbeckst commented 1 year ago

cc: @alejob @ianmkenney @IAlibay @fiona-naughton @lilyminium

orbeckst commented 11 months ago

See MDAnalysis/mdanalysis#4310 .

This issue may eventually be moved to a separate MDAKit repository.

orbeckst commented 9 months ago

@ALescoulie are you still interested in working on waterdynamics? If so, it's now in a stable MDAKit state with a release and ready to support new innovation or just good ol' refactoring.

ALescoulie commented 9 months ago

I'm interested, just been occupied working on other projects, hoping to get started on it soon after I finish my personal portfolio website and some MD-SAPT stuff.