protein_loop_session_index.md

Protein Loop Session Index

Start here after running the local loop from the repo root.

Core Links

• Root README
• Root status
• Runbook
• Evidence matrix
• Completion checklist
• Workflow map
• Architecture note
• Repo guide
• Bootstrap
• Reproducibility check
• Assessor
• Current run review
• Session index
• Next command
• Next rationale

Live State

• MOCK / DEMO only
• comparison deltas are recorded in outputs/openfold3_run_comparison.json
• run history is recorded in outputs/openfold3_run_registry.json
• follow-up artifacts are regenerated on each run

Typical Flow

1. Run python protein_loop.py --mode helical
2. Open outputs/openfold3_run_review.md
3. Open outputs/openfold3_session_index.md
4. Use the generated next command or rationale if you want the next seeded invocation