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# https://github.com/westlake-repl/SaProt/blob/main/utils/foldseek_util.py
# MIT License
# Copyright (c) 2023 westlake-repl
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import os
import json
import numpy as np
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_path: str = None,
plddt_threshold: float = 70.0,
) -> 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_path: Path to plddt file. If None, plddt will not be used.
plddt_threshold: Threshold for plddt. If plddt is lower than this value, the structure will be masked.
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}"
assert plddt_path is None or os.path.exists(
plddt_path
), f"Plddt file not found: {plddt_path}"
tmp_save_path = f"get_struc_seq_{process_id}.tsv"
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_path is not None:
with open(plddt_path, "r") as r:
plddts = np.array(json.load(r)["confidenceScore"])
# 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
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=70.0
)
print(res["A"][1].lower())
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