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import os
import time
import json
import numpy as np
import re
import sys
sys.path.append(".")
# Get structural seqs from pdb file
def get_struc_seq(foldseek,
path,
chains: list = None,
process_id: int = 0,
plddt_mask: bool = False,
plddt_threshold: float = 70.,
foldseek_verbose: bool = False) -> dict:
"""
Args:
foldseek: Binary executable file of foldseek
path: Path to pdb file
chains: Chains to be extracted from pdb file. If None, all chains will be extracted.
process_id: Process ID for temporary files. This is used for parallel processing.
plddt_mask: If True, mask regions with plddt < plddt_threshold. plddt scores are from the pdb file.
plddt_threshold: Threshold for plddt. If plddt is lower than this value, the structure will be masked.
foldseek_verbose: If True, foldseek will print verbose messages.
Returns:
seq_dict: A dict of structural seqs. The keys are chain IDs. The values are tuples of
(seq, struc_seq, combined_seq).
"""
assert os.path.exists(foldseek), f"Foldseek not found: {foldseek}"
assert os.path.exists(path), f"PDB file not found: {path}"
tmp_save_path = f"/tmp/get_struc_seq_{process_id}_{time.time()}.tsv"
if foldseek_verbose:
cmd = f"{foldseek} structureto3didescriptor --threads 1 --chain-name-mode 1 {path} {tmp_save_path}"
else:
cmd = f"{foldseek} structureto3didescriptor -v 0 --threads 1 --chain-name-mode 1 {path} {tmp_save_path}"
os.system(cmd)
seq_dict = {}
name = os.path.basename(path)
with open(tmp_save_path, "r") as r:
for i, line in enumerate(r):
desc, seq, struc_seq = line.split("\t")[:3]
# Mask low plddt
if plddt_mask:
plddts = extract_plddt(path)
assert len(plddts) == len(struc_seq), f"Length mismatch: {len(plddts)} != {len(struc_seq)}"
# Mask regions with plddt < threshold
indices = np.where(plddts < plddt_threshold)[0]
np_seq = np.array(list(struc_seq))
np_seq[indices] = "#"
struc_seq = "".join(np_seq)
name_chain = desc.split(" ")[0]
chain = name_chain.replace(name, "").split("_")[-1]
if chains is None or chain in chains:
if chain not in seq_dict:
combined_seq = "".join([a + b.lower() for a, b in zip(seq, struc_seq)])
seq_dict[chain] = (seq, struc_seq, combined_seq)
os.remove(tmp_save_path)
os.remove(tmp_save_path + ".dbtype")
return seq_dict
def extract_plddt(pdb_path: str) -> np.ndarray:
"""
Extract plddt scores from pdb file.
Args:
pdb_path: Path to pdb file.
Returns:
plddts: plddt scores.
"""
with open(pdb_path, "r") as r:
plddt_dict = {}
for line in r:
line = re.sub(' +', ' ', line).strip()
splits = line.split(" ")
if splits[0] == "ATOM":
# If position < 1000
if len(splits[4]) == 1:
pos = int(splits[5])
# If position >= 1000, the blank will be removed, e.g. "A 999" -> "A1000"
# So the length of splits[4] is not 1
else:
pos = int(splits[4][1:])
plddt = float(splits[-2])
if pos not in plddt_dict:
plddt_dict[pos] = [plddt]
else:
plddt_dict[pos].append(plddt)
plddts = np.array([np.mean(v) for v in plddt_dict.values()])
return plddts
if __name__ == '__main__':
foldseek = "/sujin/bin/foldseek"
# test_path = "/sujin/Datasets/PDB/all/6xtd.cif"
test_path = "/sujin/Datasets/FLIP/meltome/af2_structures/A0A061ACX4.pdb"
plddt_path = "/sujin/Datasets/FLIP/meltome/af2_plddts/A0A061ACX4.json"
res = get_struc_seq(foldseek, test_path, plddt_path=plddt_path, plddt_threshold=70.)
print(res["A"][1].lower()) |