portable_rdock_pipeline/check_environment.sh

#!/usr/bin/env bash
set -euo pipefail

echo "python: $(command -v python || true)"
echo "rbdock: $(command -v rbdock || true)"
echo "rbcavity: $(command -v rbcavity || true)"
echo "obabel: $(command -v obabel || true)"
echo "RDOCK_ROOT: ${RDOCK_ROOT:-}"
echo "RBT_ROOT: ${RBT_ROOT:-}"
echo "RBT_HOME: ${RBT_HOME:-}"

for exe in rbdock rbcavity obabel; do
  if ! command -v "${exe}" >/dev/null 2>&1; then
    echo "ERROR: required executable missing from PATH: ${exe}" >&2
    exit 1
  fi
done

if [ -z "${RBT_ROOT:-}" ]; then
  echo "ERROR: RBT_ROOT is not set." >&2
  exit 1
fi

python - <<'PY'
import importlib
import importlib.util
from docking_pipeline.provenance import resolve_dock_prm_path, resolve_rbt_root

required_modules = [
    "numpy",
    "pandas",
    "scipy",
    "sklearn",
    "yaml",
    "matplotlib",
    "rdkit",
    "rdkit.Chem",
    "rdkit.Chem.AllChem",
    "rdkit.Chem.Descriptors",
    "rdkit.Chem.rdMolDescriptors",
    "plip",
    "plip.structure.preparation",
]
missing = [name for name in required_modules if importlib.util.find_spec(name) is None]
for name in required_modules:
    print(f"{name}: {'ok' if name not in missing else 'missing'}")
if missing:
    raise SystemExit(f"Missing required Python modules: {', '.join(missing)}")

molstd = importlib.util.find_spec("rdkit.Chem.MolStandardize")
print(f"rdkit.Chem.MolStandardize: {'ok' if molstd is not None else 'missing_optional'}")

root = resolve_rbt_root(executable="rbdock")
print(f"resolved_rbt_root: {root or ''}")
if not root:
    raise SystemExit("No valid rDock data root detected.")
prm = resolve_dock_prm_path(executable="rbdock")
print(f"resolved_dock_prm: {prm or ''}")
if prm is None:
    raise SystemExit("Could not resolve dock.prm from the detected rDock installation.")
PY

rbdock -h >/tmp/portable_rdock_rbdock_help.stdout 2>/tmp/portable_rdock_rbdock_help.stderr || true
if ! grep -q "Usage:" /tmp/portable_rdock_rbdock_help.stdout; then
  echo "ERROR: rbdock executable is on PATH but did not print expected help." >&2
  cat /tmp/portable_rdock_rbdock_help.stdout >&2 || true
  cat /tmp/portable_rdock_rbdock_help.stderr >&2 || true
  exit 1
fi
rbcavity -h >/tmp/portable_rdock_rbcavity_help.stdout 2>/tmp/portable_rdock_rbcavity_help.stderr || true
if ! grep -q "Usage:" /tmp/portable_rdock_rbcavity_help.stdout; then
  echo "ERROR: rbcavity executable is on PATH but did not print expected help." >&2
  cat /tmp/portable_rdock_rbcavity_help.stdout >&2 || true
  cat /tmp/portable_rdock_rbcavity_help.stderr >&2 || true
  exit 1
fi
obabel -V >/tmp/portable_rdock_obabel_version.stdout 2>/tmp/portable_rdock_obabel_version.stderr || {
  echo "ERROR: obabel executable is on PATH but failed to start." >&2
  cat /tmp/portable_rdock_obabel_version.stderr >&2 || true
  exit 1
}

python -m docking_pipeline --help >/dev/null
python scripts/prepare_pdb_ligand_dataset.py --help >/dev/null

echo "Environment check completed."