Symmetry-corrected RMSD calculations

[RMeli]

This PR is an attempt to add a SymmRMSD class for symmetry-corrected RMSD calculations, powered by spyrmsd. For the time being, I created a separate class from the mainRMSD class because I believe the scope of symmetry-corrected RMSD calculations is much more narrow (and because there are some open issues with the current RMSD class, such as #2891).

Tests are currently missing, see MDAnalysis/MDAnalysisData#45.

Example usage:

import MDAnalysis as mda
from MDAnalysis.analysis import align, rms

from matplotlib import pyplot as plt

mobile = mda.Universe("npt_prod1.tpr", "npt_prod1.xtc")
ref = mda.Universe("npt_prod1.tpr", "npt_prod1.xtc", frame=0)

R = rms.RMSD(mobile, ref, select='name CA', groupselections=["resname LIG"])
R.run()

# Align trajectory to reference
# This is done internally by rms.RMSD, but it is not accessible
# See https://github.com/MDAnalysis/mdanalysis/issues/2891
_ = align.AlignTraj(mobile, ref, select='name CA',in_memory=True).run()

sR = rms.SymmRMSD(mobile, ref, select="resname LIG")
sR.run()

plt.figure()
plt.plot(R.results.rmsd[:,0], R.results.rmsd[:,-1], label="RMSD")
plt.plot(sR.results.rmsd[:,0], sR.results.rmsd[:,-1], label="SymmRMSD")
plt.legend()
plt.savefig("rmsd.png")

This is still very much WIP, but early comments/suggestions/criticisms are very welcome.

TODOs:

• Allow to compute weighted RMSD
• Documentation

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?

[pep8speaks]

Hello @RMeli! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/analysis/rms.py:

Line 782:80: E501 line too long (82 > 79 characters)

Comment last updated at 2022-06-24 22:42:34 UTC

[IAlibay]

Just a couple of pre review comments

[RMeli]

Closing in favor of a MDAKit (WIP): https://github.com/RMeli/spyrmsdkit