getting the missing gene names from uniprot

app.py

@@ -49,7 +49,7 @@ def format_search_result(raw_result):
     value = raw_result["score"]
     gene_name, species = get_gene_name(pdb_id=prot, chain_id=chain)
     key = f"PDB: {prot}.{chain}"
-    if gene_name != "Unknown":
+    if gene_name is not None:
         key += f" | Gene: {gene_name} | Organism: {species}"
     return key, value
 

protein_viz.py

@@ -55,19 +55,35 @@ def get_polymer_entity_id(chain_id, pdb_id):
 
 
 def get_gene_name_from_polymer_entity(pdb_id, entity_id):
+    gene_name, species = None, None
     if entity_id:
         url = f"https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{entity_id}"
         response = requests.get(url, timeout=1)
         if response.ok:
             res_data = response.json()
-            try:
-                source_organism = res_data["rcsb_entity_source_organism"][0]
-                gene_name = source_organism["rcsb_gene_name"][0]["value"]
-                species = source_organism["scientific_name"]
-                return gene_name, species
-            except KeyError:
-                pass
-    return "Unknown", "Unknown"
+            uniprot_id = _extract_uniprot_id(res_data)
+            source_organism = res_data.get("rcsb_entity_source_organism", [{}])[0]
+            gene_name = source_organism.get("rcsb_gene_name", [{}])[0].get("value")
+            species = source_organism.get("scientific_name")
+            if gene_name is None and uniprot_id is not None:
+                gene_name = get_gene_name_from_uniprot(uniprot_id)
+    return gene_name, species
+
+
+def get_gene_name_from_uniprot(uniprot_id):
+    gene_name = None
+    url = f"https://rest.uniprot.org/uniprotkb/{uniprot_id}"
+    response = requests.get(url, timeout=1.0)
+    if response.ok:
+        uniprot_data = response.json()
+        gene_name = uniprot_data.get("genes", [{}])[0].get("geneName", {}).get("value")
+    return gene_name
+
+
+def _extract_uniprot_id(res_data):
+    ids = res_data.get("rcsb_polymer_entity_container_identifiers", {})
+    uniprot_id = ids.get("uniprot_ids", [None])[0]
+    return uniprot_id
 
 
 def get_protein_name(pdb_id: str):