RFE: measure rmsd command

[Tristan Croll]

Fairly trivial to implement, but unless I've just failed to find it it seems to be missing from the available commands. matchmaker and align of course report the RMSD after aligning two selections, but it's often useful to get the RMSD between two selections without aligning. For example, after aligning two models with matchmaker I wanted to get the RMSD of a helix whose relative position differs substantially, but couldn't find a ready-made command available.

[pett]

I thought "move nothing" in the align command might do it, but it reports the RMSD as if the atoms had moved without actually moving them.

[pett]

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.

[pett]

Adding Hrvoje Rimac to this ticket requesting an "rmsd" command equivalent

[pett]

Implemented basic rmsd command that does not account for symmetry. Syntax: rmsd spec1 to spec2. Will open separate ticket for accounting for symmetry in RMSD computation.