Cache customised residue axes topology for frame covariance #374

Goal

Cache static residue axes topology so customised residue covariance avoids repeated MDAnalysis topology selection inside the frame loop.

Background

After caching customised united-atom axes topology, profiling shows the residue axes path is the next similar hotspot. The current path repeatedly selects residue heavy atoms, calculates UA masses, and checks neighbouring-residue bonds, even though these relationships are static across frames.

Scope

• Add cached residue topology to shared_data["axes_topology"].
• Cache only frame-independent data:
• Add unit tests and confirm regression outputs remain unchanged.
  • residue heavy atom indices
  • residue UA masses
  • neighbouring-residue bond status
• Add a cached residue axes path, e.g. get_residue_axes_from_topology(...).
• Use the cached path in FrameCovarianceNode when available.
• Keep get_residue_axes(...) as the fallback.
• Do not change force, torque, covariance, entropy, Dask, or scheduling logic.