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="${PROJECT_ROOT}/outputs/example_2_outputs"11if [ ! -d "$output_dir" ]12then13    mkdir -p "$output_dir"14fi15 16path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl"17path_for_assigned_chains=$output_dir"/assigned_pdbs.jsonl"18chains_to_design="A B"19 20python "${PROJECT_ROOT}/scripts/helper_scripts/parse_multiple_chains.py" --input_path="$folder_with_pdbs" --output_path="$path_for_parsed_chains"21 22python "${PROJECT_ROOT}/scripts/helper_scripts/assign_fixed_chains.py" --input_path="$path_for_parsed_chains" --output_path="$path_for_assigned_chains" --chain_list "$chains_to_design"23 24python "${PROJECT_ROOT}/scripts/inference.py" \25        --jsonl_path "$path_for_parsed_chains" \26        --chain_id_jsonl "$path_for_assigned_chains" \27        --out_folder "$output_dir" \28        --num_seq_per_target 2 \29        --sampling_temp "0.1" \30        --seed 37 \31        --batch_size 1 \32        --path_to_model_weights "${PROJECT_ROOT}/weight/vanilla_model_weights"33