| #!/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 "${CONDA_BASE}/etc/profile.d/conda.sh" ]; then |
| echo "ERROR: could not locate conda.sh" >&2 |
| exit 1 |
| fi |
| |
| source "${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 > "${CONDA_PREFIX}/etc/conda/deactivate.d/portable_rdock_pipeline.sh" <<'EOF' |
| |
| unset PORTABLE_RDOCK_PIPELINE_ROOT |
| unset RDOCK_ROOT |
| unset RBT_ROOT |
| unset RBT_HOME |
| EOF |
|
|
| chmod +x "${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" |
|
|
