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MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
https://mdanalysis.org
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Unifying the input for the RMSD and RMSF #2675

Open xiki-tempula opened 4 years ago

xiki-tempula commented 4 years ago

Is your feature request related to a problem?

The MDAnalysis.analysis.rms.RMSD accepts both AtomGroup or Universe but MDAnalysis.analysis.rms.RMSF only accepts AtomGroup.

Describe the solution you'd like

I think the RMSF should accept Universe as input as well. When Universe is given to RMSF as input, all the atoms in the Universe will be considered, which is the behaviour of RMSD when given a Universe.

Describe alternatives you've considered

Or perhaps force both RMSD and RMSF to accept atom group and give an exception that only atom group will be accepted, when given a universe.

lilyminium commented 4 years ago

In general a more similar interface to RMSD would be convenient; passing in a Universe and a select string to select from the Universe atoms for example, or passing in a reference and ref_frame and aligning on-the-fly.

orbeckst commented 4 years ago

I think many novice users would really like it if RMSF were to perform at least the superposition and then these additional arguments https://github.com/MDAnalysis/mdanalysis/issues/2675#issuecomment-622173334 would be needed.

(Making trajectories whole is still awkward because the performance is low, maybe @richardjgowers 's NumFOCUS summer project will fix this.)