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Commit History
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feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron
38e4510
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feat(export): add downloads to ADMET, MD, pairwise, AlphaFold, docking, pathway, plus 4 new learn topics
527a85d
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Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data
- Pipeline: lazy litellm loading in interpreter/llm_client, brace-safe prompt building, EBI MSA best-effort (clustalo->muscle) + in-process progressive MSA fallback (msa_fallback.py), robust polling with consecutive-failure detection in PipelineResults. - ADMET: SwissADME-parity block (BOILED-Egg polygons, ESOL, Martin bioavailability, Muegge, radar, SA score), HBA as pure N+O count, recharts radar/BOILED-Egg/range-bar panel, chemical name in header. - PubChem: /api/admet/search autocomplete + name/CID->SMILES resolution, debounced compound search box on ADMET page. - Docking: ligand essential-data table (formula, MW, heavy atoms, H count, HBA/HBD/TPSA/RB/LogP) and per-pose hydrogen counts. - Pin backend start scripts to backend/.venv.5bb077e
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Refine design system: semantic color tokens, tiered motion, denser result cards, VinaLog toolbar
5e98b5a
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refactor(icons): migrate lucide-react to @phosphor-icons/react, remove dep
349f22c
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fix(frontend): clear stale results, prefill-only bridges, and results-ready banners
Stop bridge pages from auto-running searches on navigation, clear result cards when inputs change, and add completion banners with auto-scroll on polling job pages. Co-authored-by: Cursor <cursoragent@cursor.com>bc59cdc -
feat(frontend): roll design-system classes across all dashboard pages + fix sidebar toggle alignment
6c03381
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feat: cross-feature auto-fill bridges — data flows between all tools via sessionStorage
- Structure page: reads structure_query, auto-fetches, cross-links to Docking/MD/Function/Domains - UniProt page: reads uniprot_accession, auto-searches, cross-links to Domains/Structure/Interactions - Interactions page: reads interaction_gene, auto-submits - ADMET page: reads admet_smiles, auto-analyzes, cross-links to Docking - Function page: reads function_pdb_id, auto-predicts - MD page: reads md_pdb_id, auto-runs - Pathway page: reads pathway_query, auto-searches - Docking page: reads docking_pdb_id and docking_smiles - BLAST page: reads domains_accession (fixes broken Domains->BLAST bridge) - Job detail page: cross-links to Domains/Structure/Interactions/Docking/MD/Function - Domains page: adds Pathway bridge712d7a9
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feat: ADMET 3a/3b split — mark RDKit descriptors as production, toxicity/ADMET as rule-based heuristic
fe8fda4
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feat: industrial-grade ADMET + detailed MD/function results
Backend (admet.py): - 50+ molecular descriptors (Fsp3, MR, volume, E-state, Wiener, Zagreb) - Full functional group analysis (12 groups) - 5 drug-likeness filters (Lipinski, Veber, Ghose, Egan, MDDR) - ADMET predictions: absorption (oral bio, Caco-2, Pgp, HIA), distribution (Vd, BBB, PPB, CNS), metabolism (CYP panel, half-life, LipE), toxicity (AMES, hERG, DILI, skin, LD50), clearance - Structural alerts: PAINS + Brenk - Composite drug-likeness score (0-100) and toxicity risk score (0-10) - Fixed imports (removed rdFineMD, Fragkins typo) Frontend (admet/page.tsx): - Tabbed layout: Overview, Properties, Drug-likeness, ADMET, Alerts - Risk badge components (color-coded pass/fail/risk levels) - Detailed ADMET category breakdowns - Structural alert summary with progress bar Frontend (md/page.tsx): - Simulation parameters card with engine/forcefield/solvent details - Integration steps progress bars - Energy analysis with convergence + production trace - RMSD/RMSF statistics (min/max/avg) …24c3fcb -
fix: extract string from rate-limit error object to prevent React crash
7300a31
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Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend
99fb209