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.

[Elaine Meng]

This may be the same as #39, or maybe this one is broader since #39 suggests limiting to amino acid sidechains only as a more tractable problem.

[pett]

In addition to the information in #39, this paper could be useful:

ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn–Munkres Algorithm
Berhane Temelso, Joel M. Mabey, Toshiro Kubota, Nana Appiah-Padi, and George C. Shields
J Chem. Inf. Model. 2017, 57, 5, 1045–1054 doi: 10.1021/acs.jcim.6b00546
​https://pubs.acs.org/doi/10.1021/acs.jcim.6b00546

[pett]

Also:

spyrmsd: symmetry-corrected RMSD calculations in Python

​https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00455-2

Here we present a new open-source RMSD calculation tool written in Python, designed to be extremely lightweight and easy to integrate into existing software.