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docs: update METHODS.md to reflect all v0.2.x scoring changes - #55
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- Section 4.1: expand activity-likeness formula to show all 7 terms (length, charge density at pH 7.4, hydrophobic fraction, aromatic bonus, amphipathicity, helix bonus weight 0.03, cross-term) with ceiling 0.97; note charge_density_ph74 preference - Section 4.2: add μH > 0.55 risk signal (Dathe 1999); update charge_density column to charge_density_ph74 with fallback note; tabulate all 6 risk signals with increments - Section 4.3: add proline penalty threshold (>15% → −0.10, DKP/Fmoc deprotection mechanism); tabulate aggregation penalty with ramp details - New Section 4.3b: serum stability score — protease site density model for trypsin (×2), chymotrypsin (×1), elastase (×0.5); score formula and literature basis - New Section 5.2: pilot panel selection — pilot_priority formula, cytotox_penalty for HIGH_CYTOTOX_RISK tier (proxy < 0.5), net selectivity swing +0.055 - Section 8: add retrospective AUROC 0.8164; table of v0.2.x PRs #47-54 with impact - Section 10: expand references from 4 to 17; add all citations used in scoring code
…#55) - Rename 'Long cysteine repeat run' → 'Long homo-repeat run (any AA)'; fix deduction from −0.15 to −0.10 flat (code: synthesis.py repeat_run >= 5 → score -= 0.10) - Fix cysteine fraction threshold from 0.15 to 0.20; fix deduction from scaled formula to −0.15 flat (code: cys > 0.20 → score -= 0.15) - Fix aggregation propensity trigger from >0.2 to >0.0; fix formula from 0.20×(prop−0.2)/0.8 to min(agg×0.25, 0.20) — linear ramp from zero, capped −0.20 - Add missing length penalties: length>30 (up to −0.40 ramp), length<8 (−0.30 flat) — the length>30 penalty is the largest single deduction possible; its absence from docs was a material omission - Fix 'five risk signals' → 'six' in safety score prose (μH signal added in PR #53) - Fix version header: 0.1.0 → 0.2.x with PR range note - Fix activity score ceiling: clarify it is the arithmetic maximum of weight sum (0.97), not an explicit min() cap — the code applies clamp01() which caps at 1.0
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Summary
charge_density_ph74preference with fallbackcharge_density_ph74; tabulated all 6 risk signals with incrementspilot_priorityformula includingcytotox_penaltyfor HIGH_CYTOTOX_RISK (proxy < 0.5), with net selectivity swingTest plan
make ci)ruff checkpasses (docs-only change; no code changed)🤖 Generated with Claude Code