genesis/structures.py

# genesis/structures.py
import requests
from typing import List, Dict

def fetch_structures_for_terms(terms: List[str]) -> List[Dict[str, str]]:
    """Fetch PDB structures from PDBe or RCSB for given search terms."""
    structures = []

    for term in terms:
        try:
            # PDBe search
            pdbe_url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select"
            params = {"q": term, "rows": 2, "wt": "json"}
            r = requests.get(pdbe_url, params=params, timeout=10)
            r.raise_for_status()
            data = r.json()

            docs = data.get("response", {}).get("docs", [])
            for doc in docs:
                pdb_id = doc.get("pdb_id")
                title = doc.get("title", term)
                if pdb_id:
                    structures.append({
                        "term": term,
                        "pdb_id": pdb_id,
                        "title": title,
                        "pdbe_url": f"https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}",
                        "rcsb_url": f"https://www.rcsb.org/structure/{pdb_id}"
                    })
        except Exception as e:
            print(f"[Structures] Failed to fetch for {term}: {e}")

    return structures