OneScience-Group/ProteinMPNN

1#!/bin/bash2 3SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"4PROJECT_ROOT="$(cd "${SCRIPT_DIR}/../.." && pwd)"5ONESCIENCE_ROOT="${ONESCIENCE_ROOT:-$(cd "${PROJECT_ROOT}/.." && pwd)}"6export PYTHONPATH="${PROJECT_ROOT}/model:${ONESCIENCE_ROOT}/src:${PYTHONPATH:-}"7 8folder_with_pdbs="${PROJECT_ROOT}/data/inputs/PDB_complexes/pdbs/"9 10output_dir="${PROJECT_ROOT}/outputs/example_5_outputs"11if [ ! -d "$output_dir" ]12then13    mkdir -p "$output_dir"14fi15 16 17path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl"18path_for_assigned_chains=$output_dir"/assigned_pdbs.jsonl"19path_for_fixed_positions=$output_dir"/fixed_pdbs.jsonl"20path_for_tied_positions=$output_dir"/tied_pdbs.jsonl"21chains_to_design="A C"22fixed_positions="9 10 11 12 13 14 15 16 17 18 19 20 21 22 23, 10 11 18 19 20 22"23tied_positions="1 2 3 4 5 6 7 8, 1 2 3 4 5 6 7 8" #two list must match in length; residue 1 in chain A and C will be sampled togther;24 25python "${PROJECT_ROOT}/scripts/helper_scripts/parse_multiple_chains.py" --input_path="$folder_with_pdbs" --output_path="$path_for_parsed_chains"26 27python "${PROJECT_ROOT}/scripts/helper_scripts/assign_fixed_chains.py" --input_path="$path_for_parsed_chains" --output_path="$path_for_assigned_chains" --chain_list "$chains_to_design"28 29python "${PROJECT_ROOT}/scripts/helper_scripts/make_fixed_positions_dict.py" --input_path="$path_for_parsed_chains" --output_path="$path_for_fixed_positions" --chain_list "$chains_to_design" --position_list "$fixed_positions"30 31python "${PROJECT_ROOT}/scripts/helper_scripts/make_tied_positions_dict.py" --input_path="$path_for_parsed_chains" --output_path="$path_for_tied_positions" --chain_list "$chains_to_design" --position_list "$tied_positions"32 33python "${PROJECT_ROOT}/scripts/inference.py" \34        --jsonl_path "$path_for_parsed_chains" \35        --chain_id_jsonl "$path_for_assigned_chains" \36        --fixed_positions_jsonl "$path_for_fixed_positions" \37        --tied_positions_jsonl "$path_for_tied_positions" \38        --out_folder "$output_dir" \39        --num_seq_per_target 2 \40        --sampling_temp "0.1" \41        --seed 37 \42        --batch_size 1 \43        --path_to_model_weights "${PROJECT_ROOT}/weight/vanilla_model_weights"44