model/ProteinMPNN/helper_scripts/make_bias_AA.py

import argparse


def main(args):

    import json

    import numpy as np

    bias_list = [float(item) for item in args.bias_list.split()]
    AA_list = [str(item) for item in args.AA_list.split()]

    my_dict = dict(zip(AA_list, bias_list))

    with open(args.output_path, "w") as f:
        f.write(json.dumps(my_dict) + "\n")


if __name__ == "__main__":
    argparser = argparse.ArgumentParser(
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )
    argparser.add_argument(
        "--output_path", type=str, help="Path to the output dictionary"
    )
    argparser.add_argument(
        "--AA_list", type=str, default="", help="List of AAs to be biased"
    )
    argparser.add_argument(
        "--bias_list", type=str, default="", help="AA bias strengths"
    )

    args = argparser.parse_args()
    main(args)

# e.g. output
# {"A": -0.01, "G": 0.02}