Create structures.py

genesis/structures.py

@@ -0,0 +1,33 @@
+# 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