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get_af2_and_mpnn_model_params.sh
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#!/bin/bash
#make new directory for model parameters
#e.g. bash get_model_params.sh "./model_params"
echo "Downloading LigandMPNN and proteinMPNN model weights"
echo "Please note that this script only downloads the minimal default weight files used in the design pipeline!"
echo "To download all of the proteinMPNN model weights please run the bash script found in lib/LigandMPNN/get_model_params.sh"
dir="lib/LigandMPNN/model_params"
mkdir -p $dir
#Original ProteinMPNN weights
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_002.pt -O $1"/proteinmpnn_v_48_002.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_010.pt -O $1"/proteinmpnn_v_48_010.pt"
wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_020.pt -O ${dir}"/proteinmpnn_v_48_020.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_48_030.pt -O $1"/proteinmpnn_v_48_030.pt"
#ProteinMPNN with num_edges=32
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_32_002.pt -O $1"/proteinmpnn_v_32_002.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_32_010.pt -O $1"/proteinmpnn_v_32_010.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_32_020.pt -O $1"/proteinmpnn_v_32_020.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/proteinmpnn_v_32_030.pt -O $1"/proteinmpnn_v_32_030.pt"
#LigandMPNN with num_edges=32; atom_context_num=25
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_005_25.pt -O $1"/ligandmpnn_v_32_005_25.pt"
wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_010_25.pt -O ${dir}"/ligandmpnn_v_32_010_25.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_020_25.pt -O $1"/ligandmpnn_v_32_020_25.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_030_25.pt -O $1"/ligandmpnn_v_32_030_25.pt"
#LigandMPNN with num_edges=32; atom_context_num=16
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_005_16.pt -O $1"/ligandmpnn_v_32_005_16.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_010_16.pt -O $1"/ligandmpnn_v_32_010_16.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_020_16.pt -O $1"/ligandmpnn_v_32_020_16.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_030_16.pt -O $1"/ligandmpnn_v_32_030_16.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/publication_version_ligandmpnn_v_32_010_25.pt -O $1"/publication_version_ligandmpnn_v_32_010_25.pt"
#Per residue label membrane ProteinMPNN
wget -q https://files.ipd.uw.edu/pub/ligandmpnn/per_residue_label_membrane_mpnn_v_48_020.pt -O ${dir}"/per_residue_label_membrane_mpnn_v_48_020.pt"
#Global label membrane ProteinMPNN
wget -q https://files.ipd.uw.edu/pub/ligandmpnn/global_label_membrane_mpnn_v_48_020.pt -O ${dir}"/global_label_membrane_mpnn_v_48_020.pt"
#SolubleMPNN
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_002.pt -O $1"/solublempnn_v_48_002.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_010.pt -O $1"/solublempnn_v_48_010.pt"
wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_020.pt -O ${dir}"/solublempnn_v_48_020.pt"
# wget -q https://files.ipd.uw.edu/pub/ligandmpnn/solublempnn_v_48_030.pt -O $1"/solublempnn_v_48_030.pt"
#### AF2 model weights
echo "Downloading AlphaFold2 model weights"
cd lib/alphafold
mkdir -p model_weights/params && cd model_weights/params
wget https://storage.googleapis.com/alphafold/alphafold_params_2021-07-14.tar
tar --extract --verbose --file=alphafold_params_2021-07-14.tar
cd ../../../..