Capture structure-track deps + pose entrypoint

- gpu/modal_app.py: add the `pose` local entrypoint used for the HDAC2
  pose-RMSD validation (run: `modal run gpu/modal_app.py::pose`).
- pyproject [structure] extra: add the deps we actually use locally
  (gemmi, spyrmsd, meeko, modal) for reproducibility; document the non-pip
  tools (Vina binary, open-babel) and that Boltz/cuequivariance are
  Modal-image-only.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

gpu/modal_app.py

@@ -164,6 +164,27 @@ def cofold(label: str, protein_seq: str, ligand_smiles: str, cofactor_ccds: list
 
 # ------------------------------------------------------------------------------- driver (local)
 
+@app.local_entrypoint()
+def pose() -> None:
+    """Save the predicted HDAC2/vorinostat complex for local pose-RMSD validation.
+
+    Run: `modal run gpu/modal_app.py::pose`. Weights are cached, so this is one fast GPU call.
+    The returned PDB (protein + vorinostat + Zn) is scored locally against 4LXZ by
+    scripts/pose_rmsd.py (align predicted protein to crystal, compare ligand).
+    """
+    target = "HDAC2"
+    pdb, res, drug, cofactors = TARGETS[target]
+    seq = binding_chain_sequence(pdb, res)
+    r = cofold.remote(f"{target}_{drug}_pose", seq, pubchem_smiles(drug), cofactors)
+    out = Path("data/processed/binding"); out.mkdir(parents=True, exist_ok=True)
+    if r.get("structure"):
+        dest = out / f"{target}_{drug}_pred.pdb"
+        dest.write_text(r["structure"])
+        print(f"saved {dest}; affinity={r['affinity']}, P(binder)={r['prob_binder']}")
+    else:
+        print("no structure returned")
+
+
 @app.local_entrypoint()
 def main() -> None:
     """Fan out one GPU call per (target, ligand) pair; tabulate affinities; positive-control test."""

pyproject.toml

@@ -33,11 +33,17 @@ dev = [
     "pytest>=8.0",
     "ruff>=0.5",
 ]
-# Structure-based binding track (PLAN §12). Docking tool (vina/smina) is NOT pip-installable on
-# ARM Mac — install via conda/micromamba or use a GPU AF3-class model; see docs/structure_binding_notes.md.
+# Structure-based binding track (PLAN §12); see docs/structure_binding_notes.md.
+# Non-pip tools (install separately): AutoDock Vina binary (tools/vina, from the AutoDock-Vina
+# GitHub release) and open-babel (brew). Boltz-2 + cuequivariance run only in the Modal GPU image
+# (gpu/modal_app.py), not locally.
 structure = [
-    "rdkit>=2024.3",
-    "requests>=2.31",
+    "rdkit>=2024.3",        # ligand prep, fingerprints
+    "requests>=2.31",       # PubChem / RCSB fetch
+    "gemmi>=0.6",           # structure parsing + superposition
+    "spyrmsd>=0.9",         # symmetry-corrected pose RMSD
+    "meeko>=0.7",           # production docking ligand prep
+    "modal>=1.5",           # ephemeral GPU orchestration
 ]
 
 [tool.setuptools.packages.find]