Update app.py

app.py

@@ -495,6 +495,31 @@ def main():
     else:
         st.sidebar.warning("⚠️ Upload or select structures")
     
+    # Residue trimming controls - add early so they're available when needed
+    st.sidebar.markdown("---")
+    st.sidebar.markdown("**🔧 Terminal Residue Trimming**")
+    col1, col2 = st.sidebar.columns(2)
+    with col1:
+        n_term_trim = st.number_input(
+            "N-term trim",
+            min_value=0,
+            max_value=10,
+            value=2,
+            step=1,
+            help="Number of residues to remove from 5' end",
+            key="n_term_trim"
+        )
+    with col2:
+        c_term_trim = st.number_input(
+            "C-term trim",
+            min_value=0,
+            max_value=10,
+            value=2,
+            step=1,
+            help="Number of residues to remove from 3' end",
+            key="c_term_trim"
+        )
+    
     # Load structure data
     ref_structure_data = []
     query_structure_data = []
@@ -599,7 +624,7 @@ def main():
                 
                 if selection_method == "Select by range":
                     current_selection = st.session_state['ref_selections'].get(selected_ref['name'], [])
-                    default_start = current_selection[0] + 2 if current_selection else 3
+                    default_start = current_selection[0] + n_term_trim if current_selection else 3
                     default_end = current_selection[-1] + 1 if current_selection else max(2, len(structure_info) - 2)
                     
                     c1, c2 = st.columns(2)
@@ -627,20 +652,14 @@ def main():
                         st.error("Start index must be ≤ end index")
                         
                 elif selection_method == "Select specific residues":
-                    current_selection = st.session_state['ref_selections'].get(selected_ref['name'], [])
-                    default_names = [structure_info[i]['full_name'] for i in current_selection] if current_selection else []
+                    # Always use current trim values for default selection (updates when trim values change)
+                    default_names = [structure_info[i]['full_name'] for i in range(n_term_trim, len(structure_info)-c_term_trim)]
                     
-                    #selected_names = st.multiselect(
-                    #    "Select residues",
-                    #    options=[info['full_name'] for info in structure_info],
-                    #    default=[structure_info[i]['full_name'] for i in range(2, len(structure_info)-2)],
-                    #    key=f"specific_ref_{selected_ref['name']}"
-                    #)
                     selected_names = st.multiselect(
                         "Select residues",
                         options=[info['full_name'] for info in structure_info],
-                        default=default_names if default_names else [structure_info[i]['full_name'] for i in range(2, len(structure_info)-2)],  # ✅ Use saved selection
-                        key=f"specific_ref_{selected_ref['name']}"
+                        default=default_names,
+                        key=f"specific_ref_{selected_ref['name']}_n{n_term_trim}_c{c_term_trim}"
                     )
                     
                     
@@ -705,8 +724,8 @@ def main():
                 
                 if selection_method == "Select by range":
                     current_selection = st.session_state['query_selections'].get(selected_query['name'], [])
-                    default_start = current_selection[0] + 2 if current_selection else 3
-                    default_end = current_selection[-1] + 1 if current_selection else max(2, len(structure_info) - 2)
+                    default_start = current_selection[0] + n_term_trim if current_selection else 3
+                    default_end = current_selection[-1] + 1 if current_selection else max(2, len(structure_info) - c_term_trim)
                     
                     c1, c2 = st.columns(2)
                     with c1:
@@ -733,21 +752,14 @@ def main():
                         st.error("Start index must be ≤ end index")
                         
                 elif selection_method == "Select specific residues":
-                    current_selection = st.session_state['query_selections'].get(selected_query['name'], [])
-                    default_names = [structure_info[i]['full_name'] for i in current_selection] if current_selection else []
+                    # Always use current trim values for default selection (updates when trim values change)
+                    default_names = [structure_info[i]['full_name'] for i in range(n_term_trim, len(structure_info)-c_term_trim)]
                     
-                    #selected_names = st.multiselect(
-                    #    "Select residues",
-                    #    options=[info['full_name'] for info in structure_info],
-                    #    default=[structure_info[i]['full_name'] for i in range(2, len(structure_info)-2)],
-                    #    key=f"specific_query_{selected_query['name']}"
-                    #)
-
                     selected_names = st.multiselect(
                         "Select residues",
                         options=[info['full_name'] for info in structure_info],
-                        default=default_names if default_names else [structure_info[i]['full_name'] for i in range(2, len(structure_info)-2)],  # ✅ Use saved selection
-                        key=f"specific_query_{selected_query['name']}"
+                        default=default_names,
+                        key=f"specific_query_{selected_query['name']}_n{n_term_trim}_c{c_term_trim}"
                     )
                     
                     name_to_idx = {info['full_name']: info['index'] for info in structure_info}
@@ -805,6 +817,7 @@ def main():
         window_size = 4
         window_type = "contiguous"
     
+    
     # Step 5: Run Analysis
     st.sidebar.subheader("4️⃣ Run Analysis")
     
@@ -1157,4 +1170,4 @@ Query: {row['Query']}
 
 
 if __name__ == "__main__":
-    main()
+    main()