# 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)