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

Fix docking on Windows: resolve obabel from venv, use Windows Vina binary

feat(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a)

feat(md): temperature/KE, Rg and SASA traces; fix OpenMM in deployed image

feat: add smoke-test suite — ADMET/MD/function/docking endpoint validation (27 tests)

feat: scientifically accurate MD simulation with OBC2 solvent, Kabsch RMSD, per-residue RMSF

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

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

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

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

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

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update

chore: remove unused celery dependency (worker uses threading, not Celery)

fix: make primer3-py optional (separate install step, router handles missing import gracefully)

fix: use aiohttp for Foldseek multipart upload

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation

Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)