File size: 7,298 Bytes
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def main(args):
import glob
import gzip
import json
import os
import time
import numpy as np
folder_with_pdbs_path = args.input_path
save_path = args.output_path
ca_only = args.ca_only
alpha_1 = list("ARNDCQEGHILKMFPSTWYV-")
states = len(alpha_1)
alpha_3 = [
"ALA",
"ARG",
"ASN",
"ASP",
"CYS",
"GLN",
"GLU",
"GLY",
"HIS",
"ILE",
"LEU",
"LYS",
"MET",
"PHE",
"PRO",
"SER",
"THR",
"TRP",
"TYR",
"VAL",
"GAP",
]
aa_1_N = {a: n for n, a in enumerate(alpha_1)}
aa_3_N = {a: n for n, a in enumerate(alpha_3)}
aa_N_1 = {n: a for n, a in enumerate(alpha_1)}
aa_1_3 = {a: b for a, b in zip(alpha_1, alpha_3)}
aa_3_1 = {b: a for a, b in zip(alpha_1, alpha_3)}
def AA_to_N(x):
# ["ARND"] -> [[0,1,2,3]]
x = np.array(x)
if x.ndim == 0:
x = x[None]
return [[aa_1_N.get(a, states - 1) for a in y] for y in x]
def N_to_AA(x):
# [[0,1,2,3]] -> ["ARND"]
x = np.array(x)
if x.ndim == 1:
x = x[None]
return ["".join([aa_N_1.get(a, "-") for a in y]) for y in x]
def parse_PDB_biounits(x, atoms=["N", "CA", "C"], chain=None):
"""
input: x = PDB filename
atoms = atoms to extract (optional)
output: (length, atoms, coords=(x,y,z)), sequence
"""
xyz, seq, min_resn, max_resn = {}, {}, 1e6, -1e6
for line in open(x, "rb"):
line = line.decode("utf-8", "ignore").rstrip()
if line[:6] == "HETATM" and line[17 : 17 + 3] == "MSE":
line = line.replace("HETATM", "ATOM ")
line = line.replace("MSE", "MET")
if line[:4] == "ATOM":
ch = line[21:22]
if ch == chain or chain is None:
atom = line[12 : 12 + 4].strip()
resi = line[17 : 17 + 3]
resn = line[22 : 22 + 5].strip()
x, y, z = [float(line[i : (i + 8)]) for i in [30, 38, 46]]
if resn[-1].isalpha():
resa, resn = resn[-1], int(resn[:-1]) - 1
else:
resa, resn = "", int(resn) - 1
# resn = int(resn)
if resn < min_resn:
min_resn = resn
if resn > max_resn:
max_resn = resn
if resn not in xyz:
xyz[resn] = {}
if resa not in xyz[resn]:
xyz[resn][resa] = {}
if resn not in seq:
seq[resn] = {}
if resa not in seq[resn]:
seq[resn][resa] = resi
if atom not in xyz[resn][resa]:
xyz[resn][resa][atom] = np.array([x, y, z])
# convert to numpy arrays, fill in missing values
seq_, xyz_ = [], []
try:
for resn in range(min_resn, max_resn + 1):
if resn in seq:
for k in sorted(seq[resn]):
seq_.append(aa_3_N.get(seq[resn][k], 20))
else:
seq_.append(20)
if resn in xyz:
for k in sorted(xyz[resn]):
for atom in atoms:
if atom in xyz[resn][k]:
xyz_.append(xyz[resn][k][atom])
else:
xyz_.append(np.full(3, np.nan))
else:
for atom in atoms:
xyz_.append(np.full(3, np.nan))
return np.array(xyz_).reshape(-1, len(atoms), 3), N_to_AA(np.array(seq_))
except TypeError:
return "no_chain", "no_chain"
pdb_dict_list = []
c = 0
if folder_with_pdbs_path[-1] != "/":
folder_with_pdbs_path = folder_with_pdbs_path + "/"
init_alphabet = [
"A",
"B",
"C",
"D",
"E",
"F",
"G",
"H",
"I",
"J",
"K",
"L",
"M",
"N",
"O",
"P",
"Q",
"R",
"S",
"T",
"U",
"V",
"W",
"X",
"Y",
"Z",
"a",
"b",
"c",
"d",
"e",
"f",
"g",
"h",
"i",
"j",
"k",
"l",
"m",
"n",
"o",
"p",
"q",
"r",
"s",
"t",
"u",
"v",
"w",
"x",
"y",
"z",
]
extra_alphabet = [str(item) for item in list(np.arange(300))]
chain_alphabet = init_alphabet + extra_alphabet
biounit_names = glob.glob(folder_with_pdbs_path + "*.pdb")
for biounit in biounit_names:
my_dict = {}
s = 0
concat_seq = ""
concat_N = []
concat_CA = []
concat_C = []
concat_O = []
concat_mask = []
coords_dict = {}
for letter in chain_alphabet:
if ca_only:
sidechain_atoms = ["CA"]
else:
sidechain_atoms = ["N", "CA", "C", "O"]
xyz, seq = parse_PDB_biounits(biounit, atoms=sidechain_atoms, chain=letter)
if type(xyz) != str:
concat_seq += seq[0]
my_dict["seq_chain_" + letter] = seq[0]
coords_dict_chain = {}
if ca_only:
coords_dict_chain["CA_chain_" + letter] = xyz.tolist()
else:
coords_dict_chain["N_chain_" + letter] = xyz[:, 0, :].tolist()
coords_dict_chain["CA_chain_" + letter] = xyz[:, 1, :].tolist()
coords_dict_chain["C_chain_" + letter] = xyz[:, 2, :].tolist()
coords_dict_chain["O_chain_" + letter] = xyz[:, 3, :].tolist()
my_dict["coords_chain_" + letter] = coords_dict_chain
s += 1
fi = biounit.rfind("/")
my_dict["name"] = biounit[(fi + 1) : -4]
my_dict["num_of_chains"] = s
my_dict["seq"] = concat_seq
if s < len(chain_alphabet):
pdb_dict_list.append(my_dict)
c += 1
with open(save_path, "w") as f:
for entry in pdb_dict_list:
f.write(json.dumps(entry) + "\n")
if __name__ == "__main__":
argparser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
argparser.add_argument(
"--input_path",
type=str,
help="Path to a folder with pdb files, e.g. /home/my_pdbs/",
)
argparser.add_argument(
"--output_path",
type=str,
help="Path where to save .jsonl dictionary of parsed pdbs",
)
argparser.add_argument(
"--ca_only",
action="store_true",
default=False,
help="parse a backbone-only structure (default: false)",
)
args = argparser.parse_args()
main(args)
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