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import argparse
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)
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