feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data

feat(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

fix: include smiles in docking payload dict for when ligand_smiles column is missing

fix: remove rate limiting from docking endpoint (429 error)

Phase 1: harden rate limits — JWT-aware keys, per-endpoint caps, daily limits on all job types

Phase 0c: offload large artifacts to Supabase Storage (docking, pipeline, sequencing)

Phase 0b: durable worker with FOR UPDATE SKIP LOCKED, per-type concurrency, separate container

Phase 0a: SSRF protection + auth on docking/sequencing, worker design doc

Fix _TRP_RINGS -> _TRP_RING_ATOMS name error

Docking viewer upgrade: Molstar GPU rendering, proper interaction geometry, 3D dashed-line rendering

Fix KeyError: payload['smiles'] -> payload.get('ligand_smiles')

Docking: minimal INSERT (only id/status/smiles), startup table check, migration SQL

Fix docking INSERT: only use columns guaranteed to exist in Supabase

Major docking rewrite: match frontend contract (pdb_id+smiles input, nested poses/interactions output, PDB fetch from RCSB, auto grid center)

Fix docking route mismatches: GET /status/{id}, frontend pdb URL prefix

Fix docking route: POST /api/docking/run to match frontend

Fix docking: add pdb_to_pdbqt_receptor() for protein PDBQT conversion

fix: Linux Vina binary, Open Babel PDBQT, pipeline_worker utcnow

fix: use /usr/bin/timeout OS-level command instead of Python subprocess timeout

fix: use asyncio.create_subprocess_exec with file descriptors + wait_for — no threads, no pipe buffer deadlock

fix: add vimontest timeout diagnostic with sleep test

fix: set deployed commit hash

fix: update commit hash in vimontest

chore: add deployed commit hash to vimontest for debugging

fix: use file handles instead of PIPE to avoid Vina pipe-buffer deadlock on Render

test: vimontest runs Vina with 10s timeout to diagnose hangs

fix: simplify vimontest to avoid Vina crash in request handler

fix: reliable Vina timeout via asyncio subprocess + cleanup vimontest

debug: check column positions in ATOM line

debug: show SDF and PDBQT content in vimontest

debug: step-by-step vimontest with short 10s timeout

fix: add urllib import to vimontest

debug: realistic vimontest with real PDB and SMILES

debug: check if timeout command exists

debug: add /api/docking/vimontest endpoint

fix: use asyncio.to_thread + file-based subprocess for Vina; add vina binary debug test

fix: use asyncio.create_subprocess_exec for Vina to prevent pipe deadlock; fix isoformat for PostgREST

feat: add progress callbacks to DockingTool.run() for real-time status tracking

fix: migrate docking/sequencing job store from file-backed dict to Supabase

fix: replace obabel CLI with NCI CACTUS API for SMILES→3D (eliminates all subprocess crashes)

fix: use asyncio.to_thread(subprocess.run) instead of asyncio.create_subprocess_exec (Python 3.14 compat)

fix: eliminate obabel entirely — use RDKit for SMILES→3D + Vina PDB/SDF input (avoids OOM from obabel C++ subprocess)

fix: revert to BackgroundTasks + async DockingTool.run (no threads, no pybel); pre-download vina in build.sh

fix: fully sync _worker_sync — replaces asyncio.run with subprocess.run + httpx.Client to avoid Python 3.14 thread crash

chore: add /api/docking/debug diagnostic endpoint

fix: run docking worker in thread pool to keep event loop responsive + add vina download timeout

feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page

feat: implement 8 tool bridges (F1-F8) + audit child components

fix: resolve 10 bugs in sequencing/docking pipelines