Update app.py

app.py

@@ -17,17 +17,6 @@ from transformers import EsmForMaskedLM, EsmTokenizer, AutoModel
 from utils.metric_learning_models_att_maps import Pre_encoded, FusionDTI
 from utils.foldseek_util import get_struc_seq
 
-# ───── Biopython fallback ───────────────────────────────────────
-from Bio.PDB import PDBParser, MMCIFParser
-from Bio.Data import IUPACData
-
-three2one = {k.upper(): v for k, v in IUPACData.protein_letters_3to1.items()}
-three2one.update({"SEC": "C", "PYL": "K"})
-def simple_seq_from_structure(path: str) -> str:
-    parser = MMCIFParser(QUIET=True) if path.endswith(".cif") else PDBParser(QUIET=True)
-    chain  = next(parser.get_structure("P", path).get_chains())
-    return "".join(three2one.get(res.get_resname().upper(), "X") for res in chain)
-
 # ───── global paths / args ──────────────────────────────────────
 FOLDSEEK_BIN = shutil.which("foldseek")
 os.environ["TOKENIZERS_PARALLELISM"] = "false"
@@ -306,8 +295,12 @@ def index():
             try:
                 parsed = get_struc_seq(FOLDSEEK_BIN, tmp_structure_path, None, plddt_mask=False)
                 chain  = list(parsed.keys())[0]; _, _, structure_seq = parsed[chain]
-            except Exception:
-                structure_seq = simple_seq_from_structure(tmp_structure_path)
+            except Exception as e:
+                result_html = (
+                    "<p style='color:red'><strong>Foldseek failed to extract sequence "
+                    f"from structure: {e}</strong></p>")
+                structure_seq = ""
+                
             protein_seq = structure_seq
             drug_input = request.form.get("drug_sequence", "")
             # Heuristically check if input is SMILES (not starting with [) and convert