File size: 4,761 Bytes
504d922 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 | #!/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"
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