From 4e580e611637f9635c34a3878e65b0f4f25f2670 Mon Sep 17 00:00:00 2001 From: j Date: Mon, 29 Jun 2026 01:34:01 +0700 Subject: [PATCH] chore: sync PR #102/#103 tracking + Nle regression guard - tests/test_presynth_qc.py: add assertion that Met flag contains "Nle" to guard against silent removal of norleucine recommendation (PR #102 regression guard) - docs/ROADMAP.md: add v0.7.x entries for PR #102 (Met/Nle flag) and PR #103 (ASSAY_PREREGISTRATION 5-family limitations block); list all 5 families explicitly (SEED-003 pre-existing + SEED-007/005 added) - docs/DISCOVERY_PREDICTION.md: add post-PR #102 and post-PR #103 tracking notes in reverse-chronological order; correct 5-family enumeration to include SEED-003 --- docs/DISCOVERY_PREDICTION.md | 12 ++++++++++++ docs/ROADMAP.md | 2 ++ tests/test_presynth_qc.py | 1 + 3 files changed, 15 insertions(+) diff --git a/docs/DISCOVERY_PREDICTION.md b/docs/DISCOVERY_PREDICTION.md index 4aa8bd67..72b88be1 100644 --- a/docs/DISCOVERY_PREDICTION.md +++ b/docs/DISCOVERY_PREDICTION.md @@ -803,6 +803,18 @@ No biological activity has been demonstrated. The lab is the judge.* --- +**Tracking note (post-PR #103):** ASSAY_PREREGISTRATION.md: serum stability model limitations +block extended to cover all 5 affected families — SEED-003 (pre-existing, 11 AA length edge), +SEED-007 (added: Met/Nle substitution + 11 AA length edge), SEED-008 (pre-existing, Trp steric, +13 AA length edge), SEED-009 (pre-existing, Pro-bond protease resistance), SEED-005 (added: +safety gate, hemolysis at MIC/3 mandatory, exclude from Wave 2 if HC₅₀ < 10× MIC). All +actionable limitations are now pre-registered before synthesis. + +**Tracking note (post-PR #102):** presynth_check.py: Met oxidation flag upgraded — now explicitly +recommends Nle (norleucine) substitution for oxidation-resistant synthesis, inert-atmosphere +storage, and mandatory HPLC purity check at receipt. Actionable guidance surfaces at QC report +level for all SEED-007 pilot variants (Met×1 at position 6 in all 4 sequences). + **Tracking note (post-PR #101):** EXPERT_REVIEW_PACK.md: SEED-007 and SEED-005 reviewer notes added (parallel to SEED-008/009 notes already present); SEED-007 Met oxidation risk row added to Pipeline Limitations table. All 7 families now have equal depth in both the wet-lab handoff diff --git a/docs/ROADMAP.md b/docs/ROADMAP.md index 8bad53c0..7e787a37 100644 --- a/docs/ROADMAP.md +++ b/docs/ROADMAP.md @@ -87,6 +87,8 @@ Implemented during the pre-wet-lab improvement loop (PRs #31–#54): - EXPERT_REVIEW_PACK.md: note added on new CSV columns for within-family prioritization (PR #98) - EXPERT_REVIEW_PACK.md: SEED-007 reviewer note (Met oxidation, bombolitin origin, SAR framing, top-10 slots) and SEED-005 reviewer note (lowest priority, safety margin) added; SEED-007 Met oxidation row in Pipeline Limitations table (PR #101) - WET_LAB_HANDOFF.md completed with dedicated special notes for all 7 seed families: SEED-007 (bombolitin-II, 4 pilot slots, all NOVEL, best serum stability, Met oxidation guidance, breakthrough-candidate framing), SEED-005 (cecropin-magainin hybrid, safety/serum risk note), SEED-008 (puroindoline-a, Trp aggregation handling, aromatic-mechanism CD interpretation), SEED-009 (Bac2A proline-rich, Pro coupling guidance, RPMI-parallel assay note restated as standalone); Serum Stability section header updated to "All 7 Seeds" with SEED-006 and SEED-007 table rows added; DISCOVERY_PREDICTION.md tracking updated (PR #100) +- presynth_check.py Met oxidation flag strengthened: Nle (norleucine) substitution explicitly recommended, inert-atmosphere storage, mandatory HPLC purity at receipt — actionable guidance now surfaces at QC report level for all SEED-007 pilot variants (PR #102) +- ASSAY_PREREGISTRATION.md serum stability model limitations block extended to cover all 5 affected families: SEED-003 (pre-existing, 11 AA length edge), SEED-007 (added: Met/Nle substitution + 11 AA length edge), SEED-008 (pre-existing, Trp steric, 13 AA length edge), SEED-009 (pre-existing, Pro-bond protease resistance), SEED-005 (added: safety gate, hemolysis at MIC/3 mandatory, exclude if HC₅₀ < 10× MIC); all limitations pre-registered before synthesis order (PR #103) ## v1.0 — Validated dry-lab-to-wet-lab loop diff --git a/tests/test_presynth_qc.py b/tests/test_presynth_qc.py index ac8b8a5e..439d5b91 100644 --- a/tests/test_presynth_qc.py +++ b/tests/test_presynth_qc.py @@ -104,6 +104,7 @@ def test_met_flag_in_flags_list(self): qc = check_sequence("s", "KRLMKKIGSAIKFL") met_flags = [f for f in qc.flags if "MET" in f] assert len(met_flags) == 1 + assert "Nle" in met_flags[0], "Met flag must recommend Nle substitution (regression guard for PR #102)" # ---------------------------------------------------------------------------