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_monomers/pdbs/"9 10output_dir="${PROJECT_ROOT}/outputs/example_8_outputs"11if [ ! -d "$output_dir" ]12then13    mkdir -p "$output_dir"14fi15 16path_for_bias=$output_dir"/bias_pdbs.jsonl"17#Adding global polar amino acid bias (Doug Tischer)18AA_list="D E H K N Q R S T W Y"19bias_list="1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39"20python "${PROJECT_ROOT}/scripts/helper_scripts/make_bias_AA.py" --output_path="$path_for_bias" --AA_list="$AA_list" --bias_list="$bias_list"21 22path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl"23python "${PROJECT_ROOT}/scripts/helper_scripts/parse_multiple_chains.py" --input_path="$folder_with_pdbs" --output_path="$path_for_parsed_chains"24 25python "${PROJECT_ROOT}/scripts/inference.py" \26        --jsonl_path "$path_for_parsed_chains" \27        --out_folder "$output_dir" \28        --bias_AA_jsonl "$path_for_bias" \29        --num_seq_per_target 2 \30        --sampling_temp "0.1" \31        --seed 37 \32        --batch_size 1 \33        --path_to_model_weights "${PROJECT_ROOT}/weight/vanilla_model_weights"34