Update app.py

app.py

@@ -50,8 +50,54 @@ def cpg_ratio(seq):
     expected = (g * c) / length
     return cg / expected if expected > 0 else 0
 
-def tata_box_presence(seq):
-    return int("TATA" in seq.upper())
+#def tata_box_presence(seq):
+#    return int("TATA" in seq.upper())
+def deltaG_stem_loop(seq):
+    """
+    Identify the strongest stem-loop in a DNA sequence
+    and return ΔG of the stem only (kcal/mol).
+    """
+
+    seq = seq.upper()
+    rna = seq.replace("T", "U")
+
+    # Nearest-neighbour ΔG values (kcal/mol)
+    nn = {
+        "AA": -0.9, "AU": -1.1, "UA": -1.3, "CA": -0.9,
+        "CU": -2.1, "GA": -1.3, "GU": -1.1, "UU": -0.9,
+        "AC": -0.9, "AG": -1.3, "UG": -1.5, "UC": -1.5,
+        "CC": -1.7, "CG": -2.4, "GC": -3.4, "GG": -1.5
+    }
+
+    # Reverse complement helper
+    def rc(s):
+        comp = str.maketrans("ATCG", "TAGC")
+        return s.translate(comp)[::-1]
+
+    best_stem = ""
+    deltaG = 0.0
+
+    # Search for inverted repeats (possible stems)
+    for i in range(len(seq)):
+        for j in range(i + 4, len(seq)):  # minimum 4 nt stem
+            left = rna[i:j]
+            right = rna[j:]
+            left_rc = rc(left).replace("T", "U")
+
+            if left_rc in right:
+                # calculate ΔG of this stem
+                total_DeltaG = 0.0
+                for k in range(len(left) - 1):
+                    pair = left[k:k+2]
+                    if pair in nn:
+                        total_DeltaG += nn[pair]
+
+                # Update if stronger (more negative) or first found
+                if total_DeltaG < deltaG or best_stem == "":
+                    best_stem = left
+                    deltaG = total_DeltaG
+
+    return deltaG
 
 def avg_bendability(seq):
     seq = seq.upper()