Refine 3Dmol.js interactions: avoid duplicate listeners and improve click handling

app.py

@@ -361,6 +361,9 @@ THREEDMOL_HEAD = """
     else { 
       _viewer = $3Dmol.createViewer(el, {backgroundColor: '0xffffff'}); 
       _viewer.setClickable(true);
+      _viewer.on('click', function(atom, event) {
+          if (atom && atom.index !== undefined) handleAtomClick(atom, event);
+      });
     }
   }
 
@@ -479,18 +482,16 @@ THREEDMOL_HEAD = """
       model.setHoverable(true);
     }
     
-    _viewer.on('click', function(atom, event) {
-        if (atom) handleAtomClick(atom, event);
-    });
-    
     // Disable context menu on the viewer to allow right-click deselection
     var el = document.getElementById('mol3d-container');
     el.oncontextmenu = function(e) { 
         e.preventDefault(); 
-        // If we didn't hit an atom (handled by handleAtomClick), we clear all
         if (_selectedAtoms.length > 0) {
-            // Find if there's an atom under cursor? 3Dmol's oncontextmenu is tricky.
-            // For now, simpler: right click always clears if no atom hit.
+            // If we right-clicked but handleAtomClick didn't catch an atom, clear all
+            // We use a small delay to see if handleAtomClick triggers first
+            setTimeout(() => {
+                if (_selectedAtoms.length > 0) clearSelections();
+            }, 50);
         }
         return false; 
     };