protein_loop.md

Protein Loop

Run the local demo loop from the repo root:

python protein_loop.py --mode helical
python protein_loop.py --mode mixed

What it does:

1. Reuses the current protein demo artifacts in outputs/.
2. Runs the deterministic OpenFold3 MSA weighting and feedback update.
3. Writes the run summary, local heuristic state, and append-only run registry.
4. Records the result in the workspace engineering log.
5. Also emits a comparison report with recommended next heuristic defaults.
6. Generates a compact markdown run review that bundles the summary, next command, rationale, and key artifact paths.
7. Generates a session index that points to the review and the other live handoff files.

Notes:

• helical uses the helical bundle demo artifacts.
• mixed uses the mixed alpha/beta demo artifacts.
• The workflow remains MOCK / DEMO until a real validation source is added.
• The run registry records explicit before/after deltas for the current and prior run.
• The comparison report recommends the next local heuristic defaults using a deterministic rule:
  • exploit-neff when support improves
  • expand-diversity when support drops
  • blend-best-and-latest when the run is flat
• After each run, open protein_loop_session_index.md for the shortest restart path.
• The root index is regenerated on each run and points at outputs/openfold3_run_review.md and outputs/openfold3_session_index.md.