Account for symmetry in RMSD calculation

[Elaine Meng]

Such as in the rmsd command, but possibly also in other commands that report RMSD values, such as matchmaker.

Some of the techniques from this paper could be applied to account for symmetry:

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism.
Bell EW, Zhang Y.
J Cheminform. 2019 Jun 7;11(1):40. doi: 10.1186/s13321-019-0362-7.
​​https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0362-7

but would probably have to apply it on a per-residue basis to avoid a combinatorial explosion (and implement in C++). Also, could be tricky for more than pairwise comparisons.