portable_rdock_pipeline/setup_server.sh

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

ENV_NAME="${1:-portable-rdock-pipeline}"
PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"

if ! command -v conda >/dev/null 2>&1; then
  echo "ERROR: conda not found in PATH" >&2
  exit 1
fi

export CONDA_NO_PLUGINS=true
CONDA_BASE="$(conda info --base 2>/dev/null)"
if [ -z "${CONDA_BASE}" ] || [ ! -f "${CONDA_BASE}/etc/profile.d/conda.sh" ]; then
  echo "ERROR: could not locate conda.sh" >&2
  exit 1
fi
# shellcheck disable=SC1090
source "${CONDA_BASE}/etc/profile.d/conda.sh"

resolve_rdock_layout() {
  local prefix="$1"
  local candidate
  for candidate in \
    "${prefix}/share/rdock" \
    "${prefix}/share" \
    "${prefix}"
  do
    if [ -f "${candidate}/data/RbtElements.dat" ] && [ -f "${candidate}/data/scripts/dock.prm" ]; then
      printf '%s\n' "${candidate}"
      return 0
    fi
  done
  return 1
}

resolve_rdock_from_path() {
  local exe candidate
  exe="$(command -v rbdock 2>/dev/null || true)"
  if [ -z "${exe}" ]; then
    return 1
  fi
  for candidate in \
    "$(cd "$(dirname "${exe}")/.." && pwd 2>/dev/null)/share/rdock" \
    "$(cd "$(dirname "${exe}")/.." && pwd 2>/dev/null)/share" \
    "${RBT_ROOT:-}"
  do
    if [ -n "${candidate}" ] && [ -f "${candidate}/data/RbtElements.dat" ] && [ -f "${candidate}/data/scripts/dock.prm" ]; then
      printf '%s\n' "${candidate}"
      return 0
    fi
  done
  return 1
}

if conda env list | awk '{print $1}' | grep -Fxq "${ENV_NAME}"; then
  conda activate "${ENV_NAME}"
else
  conda create -y -n "${ENV_NAME}" \
    -c conda-forge -c bioconda --strict-channel-priority \
    python=3.11 \
    numpy pandas scipy scikit-learn matplotlib pyyaml tqdm joblib biopython pytest requests \
    rdkit openbabel plip
  conda activate "${ENV_NAME}"
fi

conda install -y -c conda-forge -c bioconda --strict-channel-priority \
  numpy pandas scipy scikit-learn matplotlib pyyaml tqdm joblib biopython pytest requests \
  rdkit openbabel plip

ACTIVE_RBT_ROOT="$(resolve_rdock_layout "${CONDA_PREFIX}" || true)"
if [ -z "${ACTIVE_RBT_ROOT}" ]; then
  if conda install -y -c conda-forge -c bioconda --strict-channel-priority 'rdock=24.04.204_legacy'; then
    ACTIVE_RBT_ROOT="$(resolve_rdock_layout "${CONDA_PREFIX}" || true)"
  fi
fi
if [ -z "${ACTIVE_RBT_ROOT}" ]; then
  ACTIVE_RBT_ROOT="$(resolve_rdock_from_path || true)"
fi
if [ -z "${ACTIVE_RBT_ROOT}" ]; then
  echo "ERROR: could not locate a working rDock data directory." >&2
  echo "Checked:" >&2
  echo "  ${CONDA_PREFIX}/share/rdock" >&2
  echo "  ${CONDA_PREFIX}/share" >&2
  echo "  ${CONDA_PREFIX}" >&2
  echo "  rbdock from PATH plus RBT_ROOT" >&2
  echo "Install rDock for this platform, then rerun this script." >&2
  exit 1
fi

mkdir -p "${CONDA_PREFIX}/etc/conda/activate.d" "${CONDA_PREFIX}/etc/conda/deactivate.d"

cat > "${CONDA_PREFIX}/etc/conda/activate.d/portable_rdock_pipeline.sh" <<EOF
#!/usr/bin/env bash
export PORTABLE_RDOCK_PIPELINE_ROOT="${PROJECT_ROOT}"
export RDOCK_ROOT="${CONDA_PREFIX}"
export RBT_ROOT="${ACTIVE_RBT_ROOT}"
export RBT_HOME="${ACTIVE_RBT_ROOT}"
export PATH="\${CONDA_PREFIX}/bin:\${PATH}"
export LD_LIBRARY_PATH="\${CONDA_PREFIX}/lib:\${LD_LIBRARY_PATH:-}"
export DYLD_LIBRARY_PATH="\${CONDA_PREFIX}/lib:\${DYLD_LIBRARY_PATH:-}"
EOF

cat > "${CONDA_PREFIX}/etc/conda/deactivate.d/portable_rdock_pipeline.sh" <<'EOF'
#!/usr/bin/env bash
unset PORTABLE_RDOCK_PIPELINE_ROOT
unset RDOCK_ROOT
unset RBT_ROOT
unset RBT_HOME
EOF

chmod +x "${CONDA_PREFIX}/etc/conda/activate.d/portable_rdock_pipeline.sh" \
  "${CONDA_PREFIX}/etc/conda/deactivate.d/portable_rdock_pipeline.sh"

conda deactivate
conda activate "${ENV_NAME}"
hash -r

echo "Environment prepared: ${ENV_NAME}"
echo "RDOCK_ROOT=${CONDA_PREFIX}"
echo "RBT_ROOT=${ACTIVE_RBT_ROOT}"
echo "dock.prm=${ACTIVE_RBT_ROOT}/data/scripts/dock.prm"
python - <<'PY'
from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors, rdMolDescriptors
from plip.structure.preparation import PDBComplex
mol = Chem.MolFromSmiles("CCO")
assert mol is not None
assert AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=32).GetNumBits() == 32
print("RDKit import: ok")
print("PLIP import: ok", PDBComplex.__name__)
print("MolWt:", round(Descriptors.MolWt(mol), 3))
print("TPSA:", round(rdMolDescriptors.CalcTPSA(mol), 3))
PY
obabel -V
rbdock -h >/tmp/portable_rdock_setup_rbdock_help.stdout 2>/tmp/portable_rdock_setup_rbdock_help.stderr || true
grep -q "Usage:" /tmp/portable_rdock_setup_rbdock_help.stdout
rbcavity -h >/tmp/portable_rdock_setup_rbcavity_help.stdout 2>/tmp/portable_rdock_setup_rbcavity_help.stderr || true
grep -q "Usage:" /tmp/portable_rdock_setup_rbcavity_help.stdout
echo "Activate with: conda activate ${ENV_NAME}"
echo "Then run: bash ${PROJECT_ROOT}/check_environment.sh"