add sequence 2 smiles feature

app.py

@@ -108,6 +108,35 @@ class PeptideAnalyzer:
         self.clean_smiles_lookup = {}
         self.uaa_internal_exact = {} 
         self.uaa_internal_patterns = []
+        for uaa_name, uaa_data in specific_aminos.items():
+            code   = uaa_data["Code"]
+            smiles = uaa_data.get("SMILES", "")
+            nterm  = uaa_data.get("nterm", "")
+            cterm  = uaa_data.get("cterm", "")
+            letter = uaa_data.get("Letter")
+    
+            # keep existing full-aa lookups
+            if smiles:
+                self.exact_smiles_lookup[smiles] = code
+                clean = self._remove_stereochemistry(smiles)
+                self.clean_smiles_lookup.setdefault(clean, []).append(code)
+    
+            internal = ""
+            if cterm:
+                internal = _internal_from_cterm(cterm)
+            elif nterm:
+                internal = _internal_from_nterm(nterm)
+    
+            if internal:
+                self.exact_smiles_lookup[internal] = code
+                clean_int = self._remove_stereochemistry(internal)
+                self.clean_smiles_lookup.setdefault(clean_int, []).append(code)
+    
+                self.uaa_internal_exact[code] = internal
+                self.uaa_internal_patterns.append((_chirality_agnostic_regex(internal), code))
+    
+            if letter:
+                self.three_to_one[code] = letter
     
         for uaa_name, uaa_data in all_aminos.items():
             code   = uaa_data["Code"]