improve performance of is_independent (#1037)

* improve performance of is_independence, suggested by Cal

* address Cal comment

Author: daico007

mbuild/compound.py

@@ -1337,9 +1337,9 @@ def is_independent(self):
         else:
             # Cover the other cases
             bond_graph_dict = self.root.bond_graph._adj
-            for particle in self:
+            for particle in self.particles():
                 for neigh in bond_graph_dict[particle]:
-                    if neigh not in self:
+                    if neigh not in self.particles():
                         return False
             return True