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Running
on
T4
Running
on
T4
File size: 1,539 Bytes
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import argparse
def main(args):
import json
with open(args.input_path, 'r') as json_file:
json_list = list(json_file)
global_designed_chain_list = []
if args.chain_list != '':
global_designed_chain_list = [str(item) for item in args.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(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")
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"]]}
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