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>

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]