scripts/helper_scripts/make_bias_per_res_dict.py

import argparse
import os
import sys

_PROJECT_ROOT = os.path.abspath(os.path.dirname(__file__))
while _PROJECT_ROOT and not os.path.isdir(os.path.join(_PROJECT_ROOT, "model")):
    _PARENT = os.path.dirname(_PROJECT_ROOT)
    if _PARENT == _PROJECT_ROOT:
        break
    _PROJECT_ROOT = _PARENT
_MODEL_ROOT = os.path.join(_PROJECT_ROOT, "model")
_ONESCIENCE_ROOT = os.environ.get("ONESCIENCE_ROOT")
for _path in (_MODEL_ROOT, _PROJECT_ROOT):
    if os.path.exists(_path) and _path not in sys.path:
        sys.path.insert(0, _path)
if _ONESCIENCE_ROOT:
    _ONESCIENCE_SRC = os.path.join(_ONESCIENCE_ROOT, "src")
    for _path in (_ONESCIENCE_SRC, _ONESCIENCE_ROOT):
        if os.path.exists(_path) and _path not in sys.path:
            sys.path.insert(0, _path)

def main(args):
    import glob
    import random
    import numpy as np
    import json
    
    mpnn_alphabet = 'ACDEFGHIKLMNPQRSTVWYX'
    
    mpnn_alphabet_dict = {'A': 0,'C': 1,'D': 2,'E': 3,'F': 4,'G': 5,'H': 6,'I': 7,'K': 8,'L': 9,'M': 10,'N': 11,'P': 12,'Q': 13,'R': 14,'S': 15,'T': 16,'V': 17,'W': 18,'Y': 19,'X': 20}
     
    with open(args.input_path, 'r') as json_file:
        json_list = list(json_file)   
 
    my_dict = {}
    for json_str in json_list:
        result = json.loads(json_str)
        all_chain_list = [item[-1:] for item in list(result) if item[:10]=='seq_chain_']
        bias_by_res_dict = {}
        for chain in all_chain_list:
            chain_length = len(result[f'seq_chain_{chain}'])
            bias_per_residue = np.zeros([chain_length, 21])


            if chain == 'A':
                residues = [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15]
                amino_acids = [5, 9] #[G, L]
                for res in residues:
                    for aa in amino_acids:
                        bias_per_residue[res, aa] = 100.5

            if chain == 'C':
                residues = [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15]
                amino_acids = range(21)[1:] #[G, L]
                for res in residues:
                    for aa in amino_acids:
                        bias_per_residue[res, aa] = -100.5

            bias_by_res_dict[chain] = bias_per_residue.tolist()
        my_dict[result['name']] = bias_by_res_dict

    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("--input_path", type=str, help="Path to the parsed PDBs")
    argparser.add_argument("--output_path", type=str, help="Path to the output dictionary")

    args = argparser.parse_args()
    main(args)