Indexing-Invariant RMSD implementation

[ntampellini]

It would be nice to have a fully Python implementation of an indexing invariant RMSD metric, as per:

Pracht 2025 - https://pubs.acs.org/doi/10.1021/acs.jcim.4c02143
Carbone and Ghidini 2022 - https://www.mdpi.com/1420-3049/27/20/6884