File size: 1,589 Bytes
93b8af9 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 |
import argparse
def a_f_c(input_path, output_path, chain_list):
import json
with open(input_path.name, 'r') as json_file:
json_list = list(json_file)
global_designed_chain_list = []
if chain_list != '':
global_designed_chain_list = [str(item) for item in chain_list.split()]
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[:9]=='seq_chain'] #['A','B', 'C',...]
if len(global_designed_chain_list) > 0:
designed_chain_list = global_designed_chain_list
else:
#manually specify, e.g.
designed_chain_list = ["A"]
fixed_chain_list = [letter for letter in all_chain_list if letter not in designed_chain_list] #fix/do not redesign these chains
my_dict[result['name']]= (designed_chain_list, fixed_chain_list)
with open(output_path, 'w') as f:
f.write(json.dumps(my_dict) + '\n')
return output_path
# 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")
# argparser.add_argument("--chain_list", type=str, default='', help="List of the chains that need to be designed")
#
# args = argparser.parse_args()
# main(args)
# Output looks like this:
# {"5TTA": [["A"], ["B"]], "3LIS": [["A"], ["B"]]}
|