Change residue level MOI calculation to all atom

[ioanaapapa]

Summary

This PR closes #441 and changes the MOI calculation at the residue level to use all atoms masses and positions, rather than heavy atom positions and UA (heavy atom + hydrogens) masses. This corresponds to what we discussed in the CodeEntropy catch up meeting on 8 October 2026.

Changes

• When the residue level is the highest level of hierarchy, rotation axes correspond to vanilla principal axes and moment of inertia corresponds to vanilla all-atom moment of inertia from diagonals of MOI tensor.
• When the residue level is below the polymer level, the get_custom_residue_moment_of_inertia function uses all atom positions and masses.
• Regression tests have been updated to match the changes.

Impact

• Moment of inertia calculation is consistent between levels and is consistent with torque calculation at all levels of hierarchy.
• Entropy values are slightly higher, as below for one benzene molecule and 1 protein.
  benzene_MOIs.txt
  thioredoxin.txt