Improve RMSD function to take molecular symmetry into consideration?

Just wondering what the algorithm is behind the RMSD calculation.

The issue does not name an implementation file, test, or entry point. Start by locating the RMSD calculation in the Python package and determine which algorithm it uses, then research how molecular symmetry should affect the result. Done means the intended symmetry-aware behavior and supporting tests are clearly defined.

Written by the indexing model from the issue text.