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="${PROJECT_ROOT}/outputs/example_4_non_fixed_outputs"11if [ ! -d "$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"20chains_to_design="A C"21#The first amino acid in the chain corresponds to 1 and not PDB residues index for now.22design_only_positions="1 2 3 4 5 6 7 8 9 10, 3 4 5 6 7 8" #design only these residues; use flag --specify_non_fixed23 24python "${PROJECT_ROOT}/scripts/helper_scripts/parse_multiple_chains.py" --input_path="$folder_with_pdbs" --output_path="$path_for_parsed_chains"25 26python "${PROJECT_ROOT}/scripts/helper_scripts/assign_fixed_chains.py" --input_path="$path_for_parsed_chains" --output_path="$path_for_assigned_chains" --chain_list "$chains_to_design"27 28python "${PROJECT_ROOT}/scripts/helper_scripts/make_fixed_positions_dict.py" --input_path="$path_for_parsed_chains" --output_path="$path_for_fixed_positions" --chain_list "$chains_to_design" --position_list "$design_only_positions" --specify_non_fixed29 30python "${PROJECT_ROOT}/scripts/inference.py" \31        --jsonl_path "$path_for_parsed_chains" \32        --chain_id_jsonl "$path_for_assigned_chains" \33        --fixed_positions_jsonl "$path_for_fixed_positions" \34        --out_folder "$output_dir" \35        --num_seq_per_target 2 \36        --sampling_temp "0.1" \37        --seed 37 \38        --batch_size 1 \39        --path_to_model_weights "${PROJECT_ROOT}/weight/vanilla_model_weights"40