Fix chain center-of-mass loss weighting

[taivu1998]

Summary

Fixes #540 by removing the local weight multiplier from chain_center_of_mass_loss.

The chain center-of-mass loss was applying weight inside the squared clamp expression, and then AlphaFoldLoss applied loss.chain_center_of_mass.weight again during top-level aggregation. Because the local multiplier was inside the square, the default multimer contribution was effectively scaled by 0.05 ** 3 instead of the intended single top-level 0.05 coefficient.

Changes

• Compute the raw chain center-of-mass penalty in chain_center_of_mass_loss.
• Keep the weight argument in the function signature for config/backward compatibility, but document that top-level weighting is handled by AlphaFoldLoss.
• Add deterministic CPU regression coverage that:
  • verifies the direct loss is independent of the weight argument
  • checks the expected raw loss value for a two-chain fixture
  • verifies gradients still flow through predicted CA coordinates
• Add basic finite/nonnegative assertions to the existing optional chain COM smoke test.

Notes

This intentionally leaves config defaults and AlphaFoldLoss aggregation unchanged. It also leaves diagonal chain-pair normalization untouched, since that is a separate paper-faithfulness question from the weighting bug reported in #540.

Validation

• PYTHONPATH=/private/tmp/openfold-issue540-stubs:/private/tmp/openfold-issue540-test-deps-py310 python3 -m pytest tests/test_loss.py -k chain_center_of_mass -q
  • 2 passed, 1 skipped, 21 deselected
• PYTHONPATH=/private/tmp/openfold-issue540-stubs:/private/tmp/openfold-issue540-test-deps-py310 python3 -m py_compile openfold/utils/loss.py tests/test_loss.py
  • passed
• PYTHONPATH=/private/tmp/openfold-issue540-stubs:/private/tmp/openfold-issue540-test-deps-py310 python3 -m pytest tests/test_loss.py -q
  • 1 failed, 6 passed, 17 skipped
  • failure is an existing local setup/resource issue: missing openfold/resources/stereo_chemical_props.txt for test_find_structural_violations
• PYTHONPATH=/private/tmp/openfold-issue540-stubs:/private/tmp/openfold-issue540-test-deps-py310 python3 -m pytest tests/test_loss.py -k "not find_structural_violations" -q
  • 6 passed, 16 skipped, 2 deselected