Update app.py

app.py

@@ -498,7 +498,7 @@ def main():
     
     # Residue trimming controls - add early so they're available when needed
     st.sidebar.markdown("---")
-    st.sidebar.markdown("**🔧 Terminal Residue Trimming (Reference) **")
+    st.sidebar.markdown("**🔧 5'/3' Base Trimming (Reference) **")
     col1, col2 = st.sidebar.columns(2)
     with col1:
         n_term_trim_ref = st.number_input(
@@ -507,7 +507,7 @@ def main():
             max_value=10,
             value=2,
             step=1,
-            help="Number of residues to remove from 5' end",
+            help="Number of bases to remove from 5' end",
             key="n_term_trim_ref"
         )
     with col2:
@@ -517,14 +517,14 @@ def main():
             max_value=10,
             value=2,
             step=1,
-            help="Number of residues to remove from 3' end",
+            help="Number of bases to remove from 3' end",
             key="c_term_trim_ref"
         )
     
     
     # Residue trimming controls - add early so they're available when needed
     st.sidebar.markdown("---")
-    st.sidebar.markdown("**🔧 Terminal Residue Trimming (Query) **")
+    st.sidebar.markdown("**🔧 5'/3' Base Trimming (Query) **")
     col1, col2 = st.sidebar.columns(2)
     with col1:
         n_term_trim_query = st.number_input(
@@ -533,7 +533,7 @@ def main():
             max_value=10,
             value=2,
             step=1,
-            help="Number of residues to remove from 5' end",
+            help="Number of bases to remove from 5' end",
             key="n_term_trim_query"
         )
     with col2:
@@ -543,7 +543,7 @@ def main():
             max_value=10,
             value=2,
             step=1,
-            help="Number of residues to remove from 3' end",
+            help="Number of bases to remove from 3' end",
             key="c_term_trim_query"
         )
     
@@ -583,8 +583,8 @@ def main():
     if 'ref_auto_initialized' not in st.session_state and ref_structure_data:
         for struct in ref_structure_data:
             num_res = struct['num_residues']
-            if num_res > 4:
-                auto_selection = list(range(2, num_res - 2))
+            if num_res > n_term_trim_ref + c_term_trim_ref:
+                auto_selection = list(range(n_term_trim_ref, num_res - c_term_trim_ref))
                 st.session_state['ref_selections'][struct['name']] = auto_selection
             else:
                 st.session_state['ref_selections'][struct['name']] = list(range(num_res))
@@ -593,8 +593,8 @@ def main():
     if 'query_auto_initialized' not in st.session_state and query_structure_data:
         for struct in query_structure_data:
             num_res = struct['num_residues']
-            if num_res > 4:
-                auto_selection = list(range(2, num_res - 2))
+            if num_res > n_term_trim_query + c_term_trim_query:
+                auto_selection = list(range(n_term_trim_query, num_res - c_term_trim_query))
                 st.session_state['query_selections'][struct['name']] = auto_selection
             else:
                 st.session_state['query_selections'][struct['name']] = list(range(num_res))