File size: 3,788 Bytes
df36b14 | 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 | #!/usr/bin/env bash
# download_model_weights.sh
#
# Usage:
# bash download_model_weights.sh # Download into ./tool_weights
# bash download_model_weights.sh /path/to/dir # Custom download root directory
#
# The final directory structure will look like:
# MODELS_ROOT/
# af2/
# params_model_{1..5}.npz
# params_model_{1..5}_ptm.npz
# params_model_{1..5}_multimer_v3.npz
# LICENSE
# mpnn/
# ca_model_weights/
# soluble_model_weights/
# vanilla_model_weights/
#
# After downloading, update pxdbench/globals.py to point to these locations.
set -euo pipefail
# Set root directory for storing all model weights
MODELS_ROOT="${1:-$(pwd)/tool_weights}"
AF2_DIR="${MODELS_ROOT}/af2"
MPNN_DIR="${MODELS_ROOT}/mpnn"
echo "Model root directory: ${MODELS_ROOT}"
mkdir -p "${AF2_DIR}" "${MPNN_DIR}"
########################################
# 1. AlphaFold2 parameters
########################################
echo "==> Downloading AlphaFold2 parameters ..."
AF2_TAR="alphafold_params_2022-12-06.tar"
AF2_URL="https://storage.googleapis.com/alphafold/${AF2_TAR}"
# If AF2 parameters already exist, skip download
if compgen -G "${AF2_DIR}/params_model_1*.npz" > /dev/null; then
echo " AlphaFold2 params appear to already exist — skipping download."
else
tmp_tar="${MODELS_ROOT}/${AF2_TAR}"
echo " Downloading from: ${AF2_URL}"
curl -L "${AF2_URL}" -o "${tmp_tar}"
echo " Extracting to: ${AF2_DIR}"
tar -xf "${tmp_tar}" -C "${AF2_DIR}"
rm -f "${tmp_tar}"
echo " AlphaFold2 parameters downloaded successfully."
fi
########################################
# 2. ProteinMPNN weights
########################################
echo "==> Downloading ProteinMPNN weights ..."
TMP_DIR="$(mktemp -d)"
cleanup() {
rm -rf "${TMP_DIR}"
}
trap cleanup EXIT
echo " Cloning dauparas/ProteinMPNN (shallow clone)..."
git clone --depth 1 https://github.com/dauparas/ProteinMPNN.git "${TMP_DIR}"
# Copy each weight directory
for subdir in ca_model_weights soluble_model_weights vanilla_model_weights; do
src="${TMP_DIR}/${subdir}"
dst="${MPNN_DIR}/${subdir}"
if [ -d "${dst}" ]; then
echo " ${subdir} already exists — skipping."
else
echo " Copying ${subdir} → ${dst}"
mkdir -p "${MPNN_DIR}"
cp -r "${src}" "${dst}"
fi
done
echo " ProteinMPNN weights are ready in: ${MPNN_DIR}"
########################################
# 3. CCD cache (PXDesign release_data)
########################################
echo "==> Downloading CCD cache ..."
CCD_DIR="${1:-$(pwd)/release_data/ccd_cache}"
mkdir -p "${CCD_DIR}"
CCD_COMPONENTS_URL="https://pxdesign.tos-cn-beijing.volces.com/release_data/components.v20240608.cif"
CCD_RDKIT_URL="https://pxdesign.tos-cn-beijing.volces.com/release_data/components.v20240608.cif.rdkit_mol.pkl"
PDB_CLUSTER_URL="https://pxdesign.tos-cn-beijing.volces.com/release_data/clusters-by-entity-40.txt"
CCD_COMPONENTS_FILE="${CCD_DIR}/components.v20240608.cif"
CCD_RDKIT_FILE="${CCD_DIR}/components.v20240608.cif.rdkit_mol.pkl"
PDB_CLUSTER_FILE="${CCD_DIR}/clusters-by-entity-40.txt"
download_if_missing() {
local url="$1"
local out="$2"
if [ -f "$out" ]; then
echo " $(basename "$out") already exists — skipping."
else
echo " Downloading $(basename "$out")"
curl -L -C - "$url" -o "$out"
fi
}
download_if_missing "${CCD_COMPONENTS_URL}" "${CCD_COMPONENTS_FILE}"
download_if_missing "${CCD_RDKIT_URL}" "${CCD_RDKIT_FILE}"
download_if_missing "${PDB_CLUSTER_URL}" "${PDB_CLUSTER_FILE}"
echo " CCD cache is ready in: ${CCD_DIR}"
########################################
echo "==> All downloads completed."
echo "Model weight directories:"
echo " AF2: ${AF2_DIR}"
echo " MPNN: ${MPNN_DIR}"
echo "CCD cache: ${CCD_DIR}"
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