model/ProteinMPNN/helper_scripts/other_tools/make_omit_AA.py

import glob
import itertools
import json
import random

import numpy as np

# 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": []}}