Spaces:
Sleeping
Sleeping
| import glob | |
| import random | |
| import numpy as np | |
| import json | |
| import itertools | |
| #MODIFY this path | |
| with open('/home/justas/projects/lab_github/mpnn/data/pdbs.jsonl', '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[:9]=='seq_chain'] | |
| fixed_position_dict = {} | |
| print(result['name']) | |
| if result['name'] == '5TTA': | |
| for chain in all_chain_list: | |
| if chain == 'A': | |
| fixed_position_dict[chain] = [ | |
| [[int(item) for item in list(itertools.chain(list(np.arange(1,4)), list(np.arange(7,10)), [22, 25, 33]))], 'GPL'], | |
| [[int(item) for item in list(itertools.chain([40, 41, 42, 43]))], 'WC'], | |
| [[int(item) for item in list(itertools.chain(list(np.arange(50,150))))], 'ACEFGHIKLMNRSTVWYX'], | |
| [[int(item) for item in list(itertools.chain(list(np.arange(160,200))))], 'FGHIKLPQDMNRSTVWYX']] | |
| else: | |
| fixed_position_dict[chain] = [] | |
| else: | |
| for chain in all_chain_list: | |
| fixed_position_dict[chain] = [] | |
| my_dict[result['name']] = fixed_position_dict | |
| #MODIFY this path | |
| with open('/home/justas/projects/lab_github/mpnn/data/omit_AA.jsonl', 'w') as f: | |
| f.write(json.dumps(my_dict) + '\n') | |
| print('Finished') | |
| #e.g. output | |
| #{"5TTA": {"A": [[[1, 2, 3, 7, 8, 9, 22, 25, 33], "GPL"], [[40, 41, 42, 43], "WC"], [[50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149], "ACEFGHIKLMNRSTVWYX"], [[160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199], "FGHIKLPQDMNRSTVWYX"]], "B": []}, "3LIS": {"A": [], "B": []}} | |