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v0.5.52 — Membrane Interaction Proxy (Loop 31) - #146
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Phase 3 implementation begins. Membrane proxy uses Wimley-White interfacial (bacterial) and octanol (mammalian) scales for coarse-grained binding energy, combined with hydrophobic moment. Selectivity ratio distinguishes bacterial-preferring from hemolytic candidates. Changes: - src/openamp_foundry/simulation/membrane.py — MembraneProxy implementing VirtualAssayProxy with Wimley-White scales (Wimley & White 1996). Produces SimulationResult with bacterial/mammalian binding scores, selectivity ratio, and uncertainty. BomanBaseline clamped to [0,1]. - tests/test_membrane_proxy.py — 27 tests covering scale lookup, normalization, selectivity ratio, uncertainty, proxy contract, known-reference comparison (magainin > melittin selectivity), empty sequence, and version. - docs/50_LOOP_PLAN.md — Loop 31 marked complete, next is Loop 32. - docs/ROADMAP.md — v0.5.52 entry with all change details. - docs/METRICS_CURRENT.md — Pipeline version v0.5.52, test count 1873. - docs/ARCHITECTURE.md — simulation package map updated. 1873 tests passing (1843 existing + 30 new).
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Pre-push full suite: 1871 passed, 0 failed. Membrane proxy contract verified: magainin selectivity > melittin selectivity (known biological fact). All 27 new tests pass. No pipeline code changes — membrane proxy is in mode by default and does not affect ranking.
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Pre-push full suite: 1871 passed, 0 failed. Membrane proxy contract verified: magainin selectivity is greater than melittin selectivity. All 27 new tests pass. No pipeline code changes -- membrane proxy in info mode by default, does not affect ranking.
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Phase 3 implementation begins with a coarse-grained membrane binding energy proxy.
Primary:
src/openamp_foundry/simulation/membrane.py—MembraneProxyimplementingVirtualAssayProxywith literature-validated Wimley-White interfacial (bacterial) and octanol (mammalian) hydrophobicity scales. Combines with hydrophobic moment for amphipathicity. ReturnsSimulationResultwith bacterial/mammalian binding scores, selectivity ratio, and uncertainty.Tests: 27 tests covering scale lookup, normalization, selectivity ratio, uncertainty, proxy contract, known-reference comparison (magainin more selective than melittin), empty sequence.
Doc updates:
docs/50_LOOP_PLAN.mdLoop 31 ✅, next Loop 32.docs/ROADMAP.mdv0.5.52 entry.docs/METRICS_CURRENT.mdpipeline v0.5.52, test count 1873.docs/ARCHITECTURE.mdpackage map updated.1871 tests passing (pre-push full suite).