| |
| """ |
| Download canonical SMILES and assay outcome for all compounds in a PubChem BioAssay (AID). |
| Uses ListKey interface to handle large assays (>10,000 compounds). |
| |
| Usage: |
| python download_pubchem.py 584 --output smiles_with_outcome.csv |
| """ |
|
|
| import argparse |
| import csv |
| import sys |
| import time |
| import requests |
| from typing import Dict, Tuple |
| from io import StringIO |
|
|
| PUG_BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug" |
|
|
| def get_listkey_for_aid(aid: str) -> Tuple[str, int]: |
| """Get ListKey and size for a given AID (used to retrieve large CID sets).""" |
| url = f"{PUG_BASE}/assay/aid/{aid}/cids/JSON?list_return=listkey" |
| try: |
| resp = requests.get(url, timeout=20) |
| resp.raise_for_status() |
| data = resp.json()["IdentifierList"] |
| listkey = data["ListKey"] |
| size = data["Size"] |
| print(f"Retrieved ListKey: {listkey} with {size} CIDs.") |
| return listkey, size |
| except Exception as e: |
| print(f"Error retrieving ListKey for AID {aid}: {e}", file=sys.stderr) |
| sys.exit(1) |
|
|
| def fetch_smiles_from_listkey(listkey: str) -> Dict[int, str]: |
| """Fetch SMILES in batches using ListKey.""" |
| smiles_dict = {} |
| url = f"{PUG_BASE}/compound/listkey/{listkey}/property/SMILES/CSV" |
| try: |
| resp = requests.get(url, timeout=30) |
| resp.raise_for_status() |
| reader = csv.DictReader(StringIO(resp.text)) |
| count = 0 |
| for row in reader: |
| cid = int(row["CID"]) |
| smiles = row["SMILES"] |
| smiles_dict[cid] = smiles |
| count += 1 |
| print(f"Fetched {count} SMILES") |
| except Exception as e: |
| print(f"Error fetching SMILES: {e}", file=sys.stderr) |
| return smiles_dict |
|
|
| def fetch_outcomes_from_listkey(aid: int, listkey: str, size: int, batch_size: int, delay: float) -> Dict[int, str]: |
| """Fetch outcomes in batches using ListKey.""" |
| outcomes = {} |
| for start in range(0, size, batch_size): |
| url = f"{PUG_BASE}/assay/aid/{aid}/CSV?cid=listkey&listkey={listkey}&listkey_start={start}&listkey_count={batch_size}" |
| try: |
| resp = requests.get(url, timeout=30) |
| resp.raise_for_status() |
| reader = csv.DictReader(StringIO(resp.text)) |
| for row in reader: |
| if "PUBCHEM_CID" in row and row["PUBCHEM_CID"].isdigit(): |
| cid = int(row["PUBCHEM_CID"]) |
| outcome = row.get("PUBCHEM_ACTIVITY_OUTCOME", "Unavailable") |
| outcomes[cid] = outcome |
| print(f"Fetched outcomes for {len(outcomes)} compounds.") |
| time.sleep(delay) |
| except Exception as e: |
| print(f"Error fetching assay outcomes: {e}", file=sys.stderr) |
| sys.exit(1) |
| return outcomes |
|
|
| def write_to_csv(smiles_dict: Dict[int, str], outcomes: Dict[int, str], output_file: str): |
| """Write combined CID, SMILES, and outcome to CSV.""" |
| with open(output_file, "w", newline='') as f: |
| writer = csv.writer(f) |
| writer.writerow(["CID", "CanonicalSMILES", "AssayOutcome"]) |
| for cid, smiles in smiles_dict.items(): |
| outcome = outcomes.get(cid, "Unavailable") |
| writer.writerow([cid, smiles, outcome]) |
| print(f"Saved {len(smiles_dict)} entries to {output_file}") |
|
|
| def main(): |
| parser = argparse.ArgumentParser(description="Download SMILES and outcome using ListKey for a PubChem assay") |
| parser.add_argument("aid", help="PubChem Assay ID (AID)") |
| parser.add_argument("--output", "-o", default="smiles_with_outcome.csv", help="Output CSV file") |
| parser.add_argument("--batch-size", type=int, default=10000, help="Batch size for ListKey download") |
| parser.add_argument("--delay", type=float, default=0.5, help="Delay between batches (in seconds)") |
| args = parser.parse_args() |
|
|
| listkey, size = get_listkey_for_aid(args.aid) |
| smiles_dict = fetch_smiles_from_listkey(listkey) |
| outcomes = fetch_outcomes_from_listkey(args.aid, listkey, size, batch_size=args.batch_size, delay=args.delay) |
| write_to_csv(smiles_dict, outcomes, args.output) |
|
|
| if __name__ == "__main__": |
| main() |
|
|
