debug: check if timeout command exists

fix: use Linux timeout command instead of subprocess timeout to reliably kill Vina

debug: add /api/docking/vimontest endpoint

fix: add subprocess timeout=600, reduce exhaustiveness to 2, modes to 3

fix: reorder _download_vina before module-level vina resolution

fix: detect missing Vina binary at module level and download fallback; fail early if binary not found

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: encode grace_cutoff with strftime to avoid + in URL query param

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

fix: add TORSDOF 0 after ENDROOT (rigid ligand)

fix: right-justify charge to col 76 with {charge:>8.3f}, ad_type:>2 at 78-79

fix: pad PDBQT to 80 cols so charge field is parseable at positions 66 or 69

fix: correct PDBQT column alignment (atom name, coord pos, charge field)

fix: correct PDBQT column positions for atom serial number

fix: generate PDBQT directly from SDF (Vina binary rejects PDB/SDF input)

fix: convert SDF to PDB in Python (avoids Vina SDF parser issues)

fix: use NCI CACTUS /mol format instead of /sdf (Vina parses MOL better)

fix: strip SDF data sections (Vina parser rejects >header lines)

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: use obabel CLI subprocess for SMILES→3D (lightweight, no OOM) + Vina reads PDB receptor natively (no obabel PDBQT prep)

fix: use PDB instead of SDF for ligand (Vina SDF parser rejects RDKit tag)

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

fix: add import subprocess and use subprocess.PIPE instead of asyncio.subprocess.PIPE (Python 3.14 compat)

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: remove pybel bindings (causes segfault on Render), use obabel CLI subprocess only

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

fix: move global to first line of function (Python 3.14 SyntaxError)

fix: strip ROOT/BRANCH from receptor PDBQT (rigid-receptor compat)

fix: use low-level OB API with AddOption('r') for rigid receptor PDBQT

fix: move global OBABEL_CMD declaration to function top (Python 3.14 SyntaxError)

fix: reduce OOM by using in-process obabel bindings + lower vina exhaustiveness

fix: simplify build.sh to only pip install (no risky binary downloads) + fix vina download path

fix: obabel self-healing — openbabel-wheel in requirements, runtime pip fallback, Vina download

fix: check obabel availability early with clear error message, use OBABEL_CMD variable

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

fix: remove orphaned context = { line causing SyntaxError in deploy

feat: add query coverage, organism, and query accession to BLAST results

fix: robust Foldseek parsing, add logging, handle missing results key and variant target formats

fix: handle NCBI UNKNOWN status and add pathway_enrichment to frontend status order

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

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

feat: 4-layer audit/observability system

fix: replace dead lambda reference FTP URL with NCBI E-utilities

fix: resolve 10 bugs in sequencing/docking pipelines

Fix pipeline stuck issue: synthetic FASTQ fallback and demo mode