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v0.5.53 — Structure Ensemble Proxy (Loop 32) - #147
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Second Phase 3 simulation module. Chou-Fasman 3-state secondary structure prediction (helix/sheet/coil). Flags non-helical candidates where the helic-centric activity scorer is unreliable. Changes: - src/openamp_foundry/simulation/structure.py — StructureProxy with Chou-Fasman helix/sheet/coil propensity parameters. Generates normalized 3-state ensemble weights, raw propensities, and non_helical flag. HelicityBaseline for cheap baseline comparison. - tests/test_structure_proxy.py — 34 tests covering scale lookup, normalization, dominant state, non-helical flag, known reference comparisons (magainin helical, protegrin/tachyplesin beta-sheet, proline-rich non-helical, melittin ambiguous limitation). - docs/50_LOOP_PLAN.md — Loop 32 complete, next Loop 33. - docs/ROADMAP.md — v0.5.53 entry. - docs/METRICS_CURRENT.md — Pipeline v0.5.53, test count 1905. - docs/ARCHITECTURE.md — simulation package map updated. 1905 tests passing (1871 existing + 34 new).
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Jul 6, 2026
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Pre-push full suite: 1905 passed, 0 failed. Structure proxy verified: magainin not non-helical, protegrin and tachyplesin correctly flagged non-helical (beta-sheet). Melittin ambiguity documented as Chou-Fasman limitation. All 34 new tests pass. Module in info mode by default.
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Second Phase 3 simulation module. Chou-Fasman 3-state secondary structure prediction (helix/sheet/coil). Flags non-helical candidates where the helic-centric activity scorer is unreliable.
Primary:
src/openamp_foundry/simulation/structure.py—StructureProxywith Chou-Fasman helix/sheet/coil propensity parameters. Generates normalized 3-state ensemble weights, raw propensities, andnon_helicalflag (True if dominant state != helix or helix_weight < 0.33).HelicityBaselinefor cheap baseline comparison.Tests: 34 tests covering scale lookup, normalization, dominant state, non-helical flag, known reference comparisons (magainin helical, protegrin/tachyplesin beta-sheet, proline-rich non-helical, melittin ambiguous — documented limitation).
Doc updates: Loop 32 complete in 50_LOOP_PLAN. ROADMAP v0.5.53. METRICS_CURRENT v0.5.53, 1905 tests. ARCHITECTURE package map updated.
1905 tests passing (pre-push full suite).