Replace deepcopy with coord save/restore in CIF writing

[longleo17]

Summary

Replaces copy.deepcopy(atom_array) with a coord save/restore pattern in save_structure_cif(). For each of N_sample outputs (100-500), the old code deep-copied the entire AtomArray just to set new coordinates. The swap pattern just reassigns the .coord attribute reference — no data is copied.

Measured impact (synthetic benchmark)

• 39.5x faster on the coordinate assignment path
• Small fraction of total inference time, but eliminates 100-500 unnecessary full deep copies per run

Changes

• pxdesign/runner/dumper.py — save_structure_cif(): save original coords, assign predicted coords, write CIF, restore original

Test plan

• pytest tests/test_avoid_deepcopy_cif.py -v
• Run inference, verify CIF output is identical

[Copilot]

Pull request overview

This PR optimizes CIF dumping during inference by avoiding copy.deepcopy(atom_array) and instead temporarily swapping AtomArray.coord to the predicted coordinates while writing, then restoring the original coordinates.

Changes:

• Updated save_structure_cif() in the runner dumper to use coord save/restore instead of deep-copying the full AtomArray.
• Added a test to enforce that copy.deepcopy() is no longer used in pxdesign/runner/dumper.py and to validate the basic coord swap/restore pattern.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 1 comment.

File	Description
pxdesign/runner/dumper.py	Replaces deep-copy-based CIF writing with coord swapping for improved performance.
tests/test_avoid_deepcopy_cif.py	Adds regression tests to prevent reintroduction of copy.deepcopy() and to validate coord restoration behavior.

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[Copilot]

atom_array.coord is restored only on the happy path. If save_atoms_to_cif() raises (I/O error, invalid structure, etc.), the function exits early and leaves atom_array mutated for the rest of the run. Wrap the coord swap in a try/finally so the original coordinates are restored even on exceptions.