Add RNAcentral-Struct metadata and dataset card

.gitattributes

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README.md

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+---
+license: cc0-1.0
+task_categories:
+- text-generation
+- fill-mask
+- other
+tags:
+- RNA
+- RNAcentral
+- PDB
+- mmCIF
+- structural-biology
+- inverse-folding
+pretty_name: RNAcentral-Struct
+size_categories:
+- 1K<n<10K
+---
+
+# RNAcentral-Struct
+
+RNAcentral-Struct is a structure subset derived from the official RNAcentral PDB cross-reference table. It contains every unique PDB entry referenced by RNAcentral `current_release/id_mapping/database_mappings/pdb.tsv`, downloaded as mmCIF from official PDB mirrors.
+
+This dataset is intended for RNA structure-conditioned modeling, inverse folding, and cross-reference analysis. RNAcentral itself is a sequence and annotation resource; the 3D coordinates here come from wwPDB/RCSB/PDBe entries linked by RNAcentral.
+
+## Contents
+
+- `structures/*.cif`: 7,279 unique mmCIF files, one per four-character PDB entry ID.
+- `metadata/rnacentral_pdb.tsv`: the RNAcentral official PDB cross-reference table used to build this package.
+- `metadata/pdb_structure_mapping_all.csv`: all RNAcentral chain-level mappings to the downloaded mmCIF files.
+- `metadata/pdb_structure_mapping_downloaded.csv`: mappings whose referenced mmCIF file is present. For this release it matches the full mapping table.
+- `metadata/manifest.json`: machine-readable summary.
+- `metadata/summary.tsv`: compact summary.
+- `metadata/cif_sizes.tsv`: byte size for each downloaded mmCIF file.
+- `metadata/download_failures.json`: download failure list. This release has no failures.
+- `scripts/rnacentral_all_cif_downloader.py`: downloader used to reproduce the package.
+
+## Summary
+
+| field | value |
+|---|---:|
+| RNAcentral PDB mapping rows | 18,967 |
+| Unique RNAcentral UPI IDs | 4,750 |
+| Unique PDB/mmCIF entries | 7,279 |
+| Downloaded mmCIF files | 7,279 |
+| Download failures | 0 |
+| Uncompressed package size | ~54 GB |
+
+## Mapping Semantics
+
+RNAcentral `pdb.tsv` maps RNAcentral UPI IDs to PDB chain-level accessions such as `4UG0_L8`. The four-character prefix, `4UG0`, is the PDB entry ID and corresponds to one mmCIF file: `structures/4ug0.cif`. The suffix identifies a chain or chain-like accession within that entry. Multiple RNAcentral rows can therefore reference the same mmCIF file.
+
+## Reproducibility
+
+The source mapping file is:
+
+```text
+https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv
+```
+
+The downloader extracts unique PDB IDs from that mapping and downloads `{PDB_ID}.cif` from RCSB with PDBe fallback.
+
+## License
+
+RNAcentral sequence metadata is distributed under CC0. PDB coordinate files are redistributed according to wwPDB/RCSB/PDBe terms. Please cite RNAcentral and wwPDB/PDB resources when using this dataset.
+
+## Citation
+
+```bibtex
+@article{rnacentral2021,
+  author = {{RNAcentral Consortium}},
+  title = {{RNAcentral} 2021: secondary structure integration, improved sequence search and new member databases},
+  journal = {Nucleic Acids Research},
+  volume = {49},
+  number = {D1},
+  pages = {D212--D220},
+  year = {2021},
+  doi = {10.1093/nar/gkaa921}
+}
+```

download_all_cif.log

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+{
+  "out_dir": "/autodl-fs/data/StarLiu714_RNAcentral_all_cif",
+  "mapping_rows": 18967,
+  "unique_upi": 4750,
+  "unique_pdb_cif": 7279,
+  "workers": 32
+}
+progress 100/7,279; present=2,603; failures=0; elapsed=0.0 min
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+{
+  "source": "RNAcentral current_release database_mappings/pdb.tsv",
+  "mapping_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv",
+  "mapping_rows_all": 18967,
+  "unique_upi_all": 4750,
+  "unique_pdb_cif_all": 7279,
+  "downloaded_cif_files": 7279,
+  "downloaded_mapping_rows": 18967,
+  "downloaded_upi": 4750,
+  "failures": []
+}

download_all_cif.pid

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+21256

metadata/download_failures.json

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+[]

metadata/manifest.json

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+{
+  "source": "RNAcentral current_release database_mappings/pdb.tsv",
+  "mapping_url": "https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv",
+  "mapping_rows_all": 18967,
+  "unique_upi_all": 4750,
+  "unique_pdb_cif_all": 7279,
+  "downloaded_cif_files": 7279,
+  "downloaded_mapping_rows": 18967,
+  "downloaded_upi": 4750,
+  "failures": []
+}

metadata/summary.tsv

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+source	RNAcentral current_release database_mappings/pdb.tsv
+mapping_url	https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv
+mapping_rows_all	18967
+unique_upi_all	4750
+unique_pdb_cif_all	7279
+downloaded_cif_files	7279
+downloaded_mapping_rows	18967
+downloaded_upi	4750

scripts/rnacentral_all_cif_downloader.py

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+#!/usr/bin/env python3
+from __future__ import annotations
+
+import argparse
+import concurrent.futures
+import csv
+import hashlib
+import json
+import os
+import time
+import urllib.request
+from pathlib import Path
+
+PDB_TSV_URL = "https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv"
+RCSB_URL = "https://files.rcsb.org/download/{pdb}.cif"
+PDBe_URL = "https://www.ebi.ac.uk/pdbe/entry-files/download/{pdb}.cif"
+
+
+def download_url(url: str, target: Path, timeout: int = 180) -> None:
+    target.parent.mkdir(parents=True, exist_ok=True)
+    tmp = target.with_suffix(target.suffix + ".part")
+    if tmp.exists():
+        tmp.unlink()
+    with urllib.request.urlopen(url, timeout=timeout) as response, tmp.open("wb") as out:
+        while True:
+            chunk = response.read(1024 * 1024)
+            if not chunk:
+                break
+            out.write(chunk)
+    if tmp.stat().st_size == 0:
+        tmp.unlink(missing_ok=True)
+        raise RuntimeError(f"empty download: {url}")
+    tmp.replace(target)
+
+
+def parse_mapping(mapping_path: Path) -> tuple[list[dict[str, str]], list[str]]:
+    rows = []
+    pdb_ids = set()
+    with mapping_path.open("r", encoding="utf-8", newline="") as handle:
+        reader = csv.reader(handle, delimiter="\t")
+        for parts in reader:
+            if len(parts) < 5 or parts[1] != "PDB":
+                continue
+            upi, database, accession, taxid, rna_type = parts[:5]
+            pdb_id = accession[:4].lower()
+            if len(pdb_id) != 4:
+                continue
+            chain = accession[5:] if len(accession) > 5 and accession[4] == "_" else ""
+            rows.append({
+                "id": upi,
+                "upi": upi,
+                "pdb_id": pdb_id,
+                "pdb_chain": chain,
+                "rna_type": rna_type,
+                "taxid": taxid,
+                "pdb_accession": accession,
+                "structure_path": f"structures/{pdb_id}.cif",
+            })
+            pdb_ids.add(pdb_id)
+    return rows, sorted(pdb_ids)
+
+
+def is_valid_cif(path: Path) -> bool:
+    if not path.exists() or path.stat().st_size <= 0:
+        return False
+    try:
+        with path.open("rb") as handle:
+            head = handle.read(512)
+        return b"data_" in head[:128] or b"_atom_site" in head
+    except OSError:
+        return False
+
+
+def download_one(pdb_id: str, structures_dir: Path, retries: int = 3) -> tuple[str, bool, str, int]:
+    target = structures_dir / f"{pdb_id}.cif"
+    if is_valid_cif(target):
+        return pdb_id, True, "exists", target.stat().st_size
+    urls = [RCSB_URL.format(pdb=pdb_id.upper()), PDBe_URL.format(pdb=pdb_id.lower())]
+    last_error = ""
+    for attempt in range(1, retries + 1):
+        for url in urls:
+            try:
+                download_url(url, target)
+                if is_valid_cif(target):
+                    return pdb_id, True, "downloaded", target.stat().st_size
+                last_error = "downloaded file failed validation"
+            except Exception as exc:
+                last_error = f"{type(exc).__name__}: {exc}"
+                target.with_suffix(target.suffix + ".part").unlink(missing_ok=True)
+        time.sleep(min(10, 2 * attempt))
+    target.unlink(missing_ok=True)
+    return pdb_id, False, last_error, 0
+
+
+def sha256_file(path: Path) -> str:
+    h = hashlib.sha256()
+    with path.open("rb") as handle:
+        for chunk in iter(lambda: handle.read(1024 * 1024 * 8), b""):
+            h.update(chunk)
+    return h.hexdigest()
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--out-dir", type=Path, default=Path("/root/autodl-fs/StarLiu714_RNAcentral_all_cif"))
+    parser.add_argument("--workers", type=int, default=32)
+    parser.add_argument("--retries", type=int, default=3)
+    args = parser.parse_args()
+
+    out_dir = args.out_dir.resolve()
+    metadata_dir = out_dir / "metadata"
+    structures_dir = out_dir / "structures"
+    metadata_dir.mkdir(parents=True, exist_ok=True)
+    structures_dir.mkdir(parents=True, exist_ok=True)
+
+    mapping_path = metadata_dir / "rnacentral_pdb.tsv"
+    if not mapping_path.exists() or mapping_path.stat().st_size == 0:
+        download_url(PDB_TSV_URL, mapping_path)
+    rows, pdb_ids = parse_mapping(mapping_path)
+
+    all_mapping_csv = metadata_dir / "pdb_structure_mapping_all.csv"
+    with all_mapping_csv.open("w", encoding="utf-8", newline="") as handle:
+        fieldnames = ["id", "upi", "pdb_id", "pdb_chain", "rna_type", "taxid", "pdb_accession", "structure_path"]
+        writer = csv.DictWriter(handle, fieldnames=fieldnames)
+        writer.writeheader()
+        writer.writerows(rows)
+
+    print(json.dumps({
+        "out_dir": str(out_dir),
+        "mapping_rows": len(rows),
+        "unique_upi": len({r["upi"] for r in rows}),
+        "unique_pdb_cif": len(pdb_ids),
+        "workers": args.workers,
+    }, indent=2), flush=True)
+
+    failures = []
+    completed = 0
+    start = time.time()
+    with concurrent.futures.ThreadPoolExecutor(max_workers=args.workers) as executor:
+        futures = {executor.submit(download_one, pdb_id, structures_dir, args.retries): pdb_id for pdb_id in pdb_ids}
+        for future in concurrent.futures.as_completed(futures):
+            pdb_id, ok, status, size = future.result()
+            completed += 1
+            if not ok:
+                failures.append({"pdb_id": pdb_id, "error": status})
+            if completed % 100 == 0 or completed == len(pdb_ids):
+                downloaded = len(list(structures_dir.glob("*.cif")))
+                elapsed = max(time.time() - start, 1.0)
+                print(
+                    f"progress {completed:,}/{len(pdb_ids):,}; present={downloaded:,}; "
+                    f"failures={len(failures):,}; elapsed={elapsed/60:.1f} min",
+                    flush=True,
+                )
+
+    present = sorted(p.stem.lower() for p in structures_dir.glob("*.cif") if is_valid_cif(p))
+    present_set = set(present)
+    downloaded_mapping_csv = metadata_dir / "pdb_structure_mapping_downloaded.csv"
+    downloaded_rows = [r for r in rows if r["pdb_id"] in present_set]
+    with downloaded_mapping_csv.open("w", encoding="utf-8", newline="") as handle:
+        fieldnames = ["id", "upi", "pdb_id", "pdb_chain", "rna_type", "taxid", "pdb_accession", "structure_path"]
+        writer = csv.DictWriter(handle, fieldnames=fieldnames)
+        writer.writeheader()
+        writer.writerows(downloaded_rows)
+
+    failure_path = metadata_dir / "download_failures.json"
+    failure_path.write_text(json.dumps(failures, indent=2, ensure_ascii=False) + "\n", encoding="utf-8")
+
+    manifest = {
+        "source": "RNAcentral current_release database_mappings/pdb.tsv",
+        "mapping_url": PDB_TSV_URL,
+        "mapping_rows_all": len(rows),
+        "unique_upi_all": len({r["upi"] for r in rows}),
+        "unique_pdb_cif_all": len(pdb_ids),
+        "downloaded_cif_files": len(present),
+        "downloaded_mapping_rows": len(downloaded_rows),
+        "downloaded_upi": len({r["upi"] for r in downloaded_rows}),
+        "failures": failures,
+    }
+    (metadata_dir / "manifest.json").write_text(json.dumps(manifest, indent=2, ensure_ascii=False) + "\n", encoding="utf-8")
+    with (metadata_dir / "summary.tsv").open("w", encoding="utf-8") as handle:
+        for key, value in manifest.items():
+            if key != "failures":
+                handle.write(f"{key}\t{value}\n")
+
+    # A compact checksum file is useful for interrupted/resumed archive work.
+    with (metadata_dir / "cif_sizes.tsv").open("w", encoding="utf-8") as handle:
+        handle.write("pdb_id\tbytes\n")
+        for pdb_id in present:
+            p = structures_dir / f"{pdb_id}.cif"
+            handle.write(f"{pdb_id}\t{p.stat().st_size}\n")
+
+    print(json.dumps(manifest, indent=2, ensure_ascii=False), flush=True)
+
+
+if __name__ == "__main__":
+    main()