Datasets:
File size: 3,517 Bytes
d3f6b75 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 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 | # Some PDB entries referenced in the dataset were missing structure files.
# This might happened becuase the up-to-date SAAINT-DB dataset was generated in February 2026, while the PDB files were uploaded in January 2026.
# We identified the missing entries and downloaded 111 mmCIF files from the RCSB Protein Data Bank (PDB),
# updating the dataset to reflect the available structures as of February 2026.
import os
import requests
import time
from pathlib import Path
missing = {'10gh', '12e8', '21du', '22ps', '9d72', '9d73', '9d74', '9dz4', '9gei', '9gjg', '9i3w', '9i3x', '9i3z', '9i40', '9i41', '9i42', '9i43', '9i45', '9i4b', '9i4c', '9i4d', '9i4e', '9i5n', '9i6q', '9i9h', '9j5l', '9j87', '9jno', '9l1l', '9l8z', '9l9o', '9lqu', '9lqw', '9lqx', '9lr1', '9lr2', '9lr3', '9lrs', '9lsy', '9lsz', '9lw5', '9lwc', '9n2v', '9n38', '9n7m', '9n7o', '9n7q', '9n7s', '9n7t', '9n7v', '9n8f', '9n8i', '9n8j', '9n8n', '9ncd', '9nln', '9nnz', '9noz', '9nvg', '9nyx', '9o8m', '9o8q', '9o8r', '9o8s', '9o8t', '9oed', '9oi2', '9oi3', '9oum', '9oun', '9ouo', '9oup', '9ouq', '9our', '9ov4', '9pqs', '9psn', '9pso', '9psp', '9qrv', '9qtn', '9qto', '9ssm', '9th6', '9uaq', '9ubr', '9ucl', '9ugo', '9v0x', '9v1h', '9vjj', '9vwz', '9vz8', '9wey', '9wrn', '9ws0', '9wu2', '9xou', '9xqc', '9xqn', '9xsx', '9xth', '9y0a', '9y0d', '9y0e', '9yc5', '9yc6', '9yio', '9yy0', '9zwe', '9zz6'}
OUT_DIR = "downloaded_missing_cifs"
os.makedirs(OUT_DIR, exist_ok=True)
def download_cif(pdb_id, out_dir=OUT_DIR):
pdb_id = str(pdb_id).strip().upper()
url = f"https://files.rcsb.org/download/{pdb_id}.cif"
try:
r = requests.get(url, timeout=30)
if r.status_code == 200 and len(r.content) > 0:
out_path = os.path.join(out_dir, f"{pdb_id}.cif")
with open(out_path, "wb") as f:
f.write(r.content)
return True
else:
return False
except requests.exceptions.RequestException:
return False
def main(missing_list):
failed = []
for pid in missing_list:
success = download_cif(pid)
if not success:
failed.append(pid)
print("Total requested:", len(missing_list))
print("Downloaded CIF:", len(missing_list) - len(failed))
print("Failed:", len(failed))
if failed:
print("Example failed:", failed[:10])
if __name__ == "__main__":
missing_list = list(missing) # existing variable
main(missing_list)
# Download FASTA files for 111 missing CIFs
BASE_DIR = "database/mmCIF_divided"
OUT_DIR = "database/fasta_divided"
for folder in os.listdir(BASE_DIR):
folder_path = os.path.join(BASE_DIR, folder)
if not os.path.isdir(folder_path):
continue
code = folder
out_folder = os.path.join(OUT_DIR, code)
os.makedirs(out_folder, exist_ok=True)
for file in os.listdir(folder_path):
if not file.endswith(".cif"):
continue
pdb_id = file.replace(".cif", "")
url = f"https://www.rcsb.org/fasta/entry/{pdb_id}/display"
out_path = os.path.join(out_folder, f"{pdb_id}.fasta")
print(f"Downloading FASTA for {pdb_id}...")
try:
r = requests.get(url, timeout=30)
if r.status_code == 200 and len(r.text) > 0:
with open(out_path, "w") as f:
f.write(r.text)
else:
print(f"Failed: {pdb_id}")
except Exception as e:
print(f"Error downloading {pdb_id}: {e}")
time.sleep(0.5) |