protein_loop_workflow_map.md

Protein Loop Workflow Map

Entry Layer

• README.md
• protein_loop_session_index.md
• protein_loop_status.md
• protein_loop_runbook.md
• protein_loop_evidence_matrix.md
• protein_loop_completion_checklist.md

Live Handoff Layer

• outputs/openfold3_run_review.md
• outputs/openfold3_session_index.md
• outputs/openfold3_next_run_command.txt
• outputs/openfold3_next_run_rationale.txt

System Layer

• outputs/protein_loop_runner.py orchestrates the local loop
• outputs/openfold3_msa_weighting_pipeline.py scores, compares, and seeds the next run
• outputs/protein_loop_system_map.md documents the outputs-level workflow

State Layer

• outputs/openfold3_run_registry.json stores append-only history
• outputs/openfold3_run_comparison.json stores live deltas and next defaults
• outputs/protein_loop_run_summary.json stores the latest run summary
• protein_loop_status.md shows the current live status at a glance

Constraints

• MOCK / DEMO only
• local-first
• reproducible
• explicit overrides always win over seeded defaults