update more aa recog

app.py

@@ -236,6 +236,59 @@ class PeptideAnalyzer:
             if not any(p in content for p in ['C(C)C', 'COC', 'CN(', 'C(C)O']):
                 return 'Ala', mods
         
+        # Tyrosine (Tyr) - 4-hydroxybenzyl side chain
+        if ('Cc2ccc(O)cc2' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Tyr', mods
+        
+        # Tryptophan (Trp) - Indole side chain
+        if ('Cc2c[nH]c3ccccc23' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Trp', mods
+        
+        # Serine (Ser) - Hydroxymethyl side chain
+        if '[C@H](CO)' in content or '[C@@H](CO)' in content:
+            if not ('C(C)O' in content or 'COC' in content):
+                return 'Ser', mods
+        
+        # Threonine (Thr) - 1-hydroxyethyl side chain
+        if '[C@@H]([C@@H](C)O)' in content or '[C@H]([C@H](C)O)' in content:
+            return 'Thr', mods
+        
+        # Cysteine (Cys) - Thiol side chain
+        if '[C@H](CS)' in content or '[C@@H](CS)' in content:
+            return 'Cys', mods
+        
+        # Methionine (Met) - Methylthioethyl side chain
+        if ('C[C@H](CCSC)' in content or 'C[C@@H](CCSC)' in content):
+            return 'Met', mods
+        
+        # Asparagine (Asn) - Carbamoylmethyl side chain
+        if ('CC(=O)N' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Asn', mods
+        
+        # Glutamine (Gln) - Carbamoylethyl side chain
+        if ('CCC(=O)N' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Gln', mods
+        
+        # Aspartic acid (Asp) - Carboxymethyl side chain
+        if ('CC(=O)O' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Asp', mods
+        
+        # Glutamic acid (Glu) - Carboxyethyl side chain
+        if ('CCC(=O)O' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Glu', mods
+        
+        # Lysine (Lys) - 4-aminobutyl side chain
+        if ('C[C@H](CCCCN)' in content or 'C[C@@H](CCCCN)' in content):
+            return 'Lys', mods
+        
+        # Arginine (Arg) - 3-guanidinopropyl side chain
+        if ('CCCNC(=N)N' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'Arg', mods
+        
+        # Histidine (His) - Imidazole side chain
+        if ('Cc2cnc[nH]2' in content) and ('C[C@H]' in content or 'C[C@@H]' in content):
+            return 'His', mods
+            
         return None, mods
 
     def get_modifications(self, segment):