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# Copyright 2024 ByteDance and/or its affiliates.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import json
import os
from functools import partial
from os.path import join as opjoin
from typing import Callable, Tuple
with open("./scripts/msa/data/pdb_seqs/seq_to_pdb_id_entity_id.json", "r") as f:
seq_to_pdbid = json.load(f)
first_pdbid_to_seq = {"_".join(v[0]): k for k, v in seq_to_pdbid.items()}
with open("./scripts/msa/data/pdb_seqs/seq_to_pdb_index.json", "r") as f:
seq_to_pdb_index = json.load(f)
def rematch(pdb_line: str) -> Tuple[str, str]:
pdb_id = pdb_line[1:-1]
origin_query_seq = first_pdbid_to_seq[pdb_id]
pdb_index = seq_to_pdb_index[origin_query_seq]
return pdb_index, origin_query_seq
def write_log(
msg: str,
fname: str,
log_root: str,
) -> None:
basename = fname.split(".")[0]
with open(opjoin(log_root, f"{basename}-{msg}"), "w") as f:
pass
def process_one_file(
fname: str, msa_root: str, save_root: str, logger: Callable
) -> None:
with open(file_path := opjoin(msa_root, fname), "r") as f:
for i, line in enumerate(f):
if i == 0:
pdb_line = line
if i == 1:
if len(line) == 1:
logger("empty_query_seq", fname)
return
query_line = line
break
save_fname, origin_query_seq = rematch(pdb_line)
os.makedirs(sub_dir_path := opjoin(save_root, f"{save_fname}"), exist_ok=True)
uniref100_lines = [">query\n", f"{origin_query_seq}\n"]
other_lines = [">query\n", f"{origin_query_seq}\n"]
with open(file_path, "r") as f:
lines = f.readlines()
for i, line in enumerate(lines):
if i < 2:
continue
if i % 2 == 0:
# header
if not line.startswith(">"):
logger(f"bad_header_{i}", fname)
return
seq = lines[i + 1]
if line.startswith(">UniRef100"):
uniref100_lines.extend([line, seq])
else:
other_lines.extend([line, seq])
assert len(other_lines) + len(uniref100_lines) - 2 == len(lines)
other_lines = other_lines[0:2] + other_lines[4:]
for i, line in enumerate(other_lines):
if i > 0 and i % 2 == 0:
assert "\t" in line
with open(opjoin(sub_dir_path, "uniref100_hits.a3m"), "w") as f:
for line in uniref100_lines:
f.write(line)
with open(opjoin(sub_dir_path, "mmseqs_other_hits.a3m"), "w") as f:
for line in other_lines:
f.write(line)
if __name__ == "__main__":
msa_root = "./scripts/msa/data/mmcif_msa_with_taxid"
save_root = "./scripts/msa/data/mmcif_msa"
log_root = "./scripts/msa/data/mmcif_msa_log"
os.makedirs(log_root, exist_ok=True)
os.makedirs(save_root, exist_ok=True)
print("Loading file names...")
logger = partial(write_log, log_root=log_root)
for fname in os.listdir(msa_root):
process_one_file(
fname=fname, msa_root=msa_root, save_root=save_root, logger=logger
)
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