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feat: add Chou-Fasman helix propensity scoring (Pα) to feature pipeline - #35
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Add helix_propensity_score() using Chou-Fasman (1974) Pα parameters. The mean Pα across all residues quantifies helical-forming tendency: >1.03 is helix-forming, <0.75 is helix-breaking (Pro=0.57, Gly=0.57). All 5 pilot panel seed families rely on helical amphipathicity for membrane disruption, so this feature adds discriminative signal against proline-rich or random sequence backgrounds. - physchem.py: _HELIX_PROPENSITY table + helix_propensity_score(); exposes helix_propensity key in compute_features() return dict - activity.py: helix_bonus (max +0.01) added; amphipathicity weight reduced 0.15→0.14 to maintain score ceiling below 1.0 - tests/test_helix_propensity.py: 23 tests (Pα values, helix vs proline-rich sequences, compute_features integration, activity score fallback) - tests/test_scoring_activity.py: update hardcoded weight assertion 0.075→0.07 - docs/DISCOVERY_PREDICTION.md: mark PR #34 done, add item 5 for Chou-Fasman
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Summary
helix_propensity_score()— new function inphyschem.pycomputing the mean Chou-Fasman Pα (alpha-helix propensity) across all residues. Uses published values from Chou & Fasman (1974) Biochemistry 13:222-245. Pα > 1.0 = helix-forming, < 0.75 = helix-breaking.compute_features()exposes new keyhelix_propensity(float) for all sequences.activity_likeness_score()gains ahelix_bonus(max +0.01) for helix-forming sequences; amphipathicity weight reduced 0.15→0.14 to maintain score ceiling below 1.0.Scientific rationale
All 5 pilot panel seed families are membrane-active helical AMPs (magainin, LL-37 fragment, cecropin, temporin family). Their mechanism requires alpha-helix formation at the membrane interface. The existing hydrophobic_moment feature captures amphipathic helix arrangement but not helix propensity — a sequence can have high hydrophobic moment while being intrinsically disordered. Chou-Fasman Pα adds an orthogonal signal: does this sequence want to form a helix?
Key discriminators:
Test plan
pytest tests/test_helix_propensity.py— 23/23 passhelix_propensity_score("AAAAAAAAAA")== 1.42 (poly-Ala = pure helix-former)helix_propensity_score("GNRPVYIPQPRPPHPR")< 1.0 (apidaecin, Pro-rich)helix_propensity_score("KWKLFKKIGAVLKVL")> 1.0 (magainin analog, helical AMP)helix_propensitydefault to 1.0 (indifferent)