fix: address code review issues on PR #51

- Add TestHelixBonusWeight with 3 numeric tests that pin the 0.03 helix
  bonus weight: exact delta at helix_pa=1.20, half-value at pa=1.10,
  and score ceiling assertion at 0.97
- Add test_proline_stacks_with_aggregation_propensity to cover combined
  agg+pro penalty interaction
- Fix synthesis.py docstring: DKP formation is N-terminal dipeptide risk
  during piperidine deprotection, not exclusive to XP junction coupling
- Makefile: bump test count to 1168

Author: cschanhniem

Makefile

@@ -20,7 +20,7 @@ lint:
 	$(RUFF) check src tests scripts
 
 ci: lint test
-	@echo "CI passed: lint + 1164-test suite green"
+	@echo "CI passed: lint + 1168-test suite green"
 
 bench-leakage:
 	PYTHONPATH=src $(PYTHON) -m openamp_foundry.cli bench leakage \

src/openamp_foundry/scoring/synthesis.py

@@ -14,10 +14,11 @@ def synthesis_feasibility_score(features: dict, valid_sequence: bool = True) ->
     - Aggregation propensity > 0: interior hydrophobic runs (VILMFW ≥ 4) and high
       beta-branched density (Val/Ile/Thr) cause on-resin aggregation and poor solubility.
       References: Quittot et al. (2017) Protein Sci; Wurth et al. (2006) J Mol Biol.
-    - Proline fraction > 15%: N-methylated backbone requires extended activation; XP junctions
-      prone to diketopiperazine (DKP) formation during Fmoc SPPS; overall coupling efficiency
-      reduced. References: Barlos et al. (1989) Int J Peptide Protein Res; Quibell et al.
-      (1994) J Am Chem Soc; Fischer (2003) Curr Opin Drug Discov Devel.
+    - Proline fraction > 15%: N-methylated backbone requires extended activation (slow couplings
+      at XP junctions); DKP formation risk at N-terminal dipeptides containing Pro during
+      piperidine Fmoc deprotection; overall coupling efficiency reduced. References: Barlos et
+      al. (1989) Int J Peptide Protein Res; Quibell et al. (1994) J Am Chem Soc; Fischer (2003)
+      Curr Opin Drug Discov Devel.
     """
     if not valid_sequence:
         return 0.0

tests/test_scoring_activity.py

@@ -255,6 +255,37 @@ def test_dual_property_amps_score_higher_than_single_property(self):
         assert dual > only_amph
 
 
+class TestHelixBonusWeight:
+    def test_helix_bonus_weight_0_03(self):
+        # helix_pa=1.20 → clamp01((1.20-1.0)/0.20)=1.0 → bonus=1.0*0.03=0.03
+        base = {
+            "length": 18, "charge_density": 0.30, "hydrophobic_fraction": 0.45,
+            "aromatic_fraction": 0.0, "hydrophobic_moment": 0.0,
+        }
+        s_no_helix = activity_likeness_score({**base, "helix_propensity": 1.0})
+        s_full_helix = activity_likeness_score({**base, "helix_propensity": 1.20})
+        assert abs((s_full_helix - s_no_helix) - 0.03) < 0.001
+
+    def test_helix_bonus_partial_at_pa_110(self):
+        # helix_pa=1.10 → clamp01(0.10/0.20)=0.5 → bonus=0.5*0.03=0.015
+        base = {
+            "length": 18, "charge_density": 0.30, "hydrophobic_fraction": 0.45,
+            "aromatic_fraction": 0.0, "hydrophobic_moment": 0.0,
+        }
+        s_no_helix = activity_likeness_score({**base, "helix_propensity": 1.0})
+        s_half_helix = activity_likeness_score({**base, "helix_propensity": 1.10})
+        assert abs((s_half_helix - s_no_helix) - 0.015) < 0.001
+
+    def test_score_ceiling_is_0_97(self):
+        # All components at maximum: ceiling = 0.24+0.27+0.17+0.10+0.14+0.03+0.02 = 0.97
+        all_max = {
+            "length": 18, "charge_density": 0.50, "hydrophobic_fraction": 0.45,
+            "aromatic_fraction": 0.20, "hydrophobic_moment": 0.80,
+            "helix_propensity": 1.20,
+        }
+        assert activity_likeness_score(all_max) == 0.97
+
+
 class TestKnownAMPs:
     def test_magainin_like_scores_well(self):
         # KWKLFKKIGAVLKVL — canonical AMP-like sequence

tests/test_scoring_synthesis.py

@@ -134,3 +134,12 @@ def test_proline_penalty_stacks_with_other_penalties(self):
         feat = {"length": 15, "longest_repeat_run": 5, "cysteine_fraction": 0.25, "proline_fraction": 0.20}
         score = synthesis_feasibility_score(feat)
         assert abs(score - 0.65) < 0.001
+
+    def test_proline_stacks_with_aggregation_propensity(self):
+        # agg=0.4: min(0.4*0.25, 0.20)=0.10 penalty; pro=0.20: 0.10 penalty → 1.0-0.20=0.80
+        feat = {
+            "length": 15, "longest_repeat_run": 1, "cysteine_fraction": 0.0,
+            "aggregation_propensity": 0.4, "proline_fraction": 0.20,
+        }
+        score = synthesis_feasibility_score(feat)
+        assert abs(score - 0.80) < 0.001