Don't modify bond dict while iterating over it.

Fixes this problem:

Error: Problem family: Surface_Adsorption_vdW
Error: Problem reactants: (Molecule(smiles="[Pt]"), Molecule(smiles="CO"))
Traceback (most recent call last):
snip
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1567, in _generate_product_structures
    product_structures = self.apply_recipe(reactant_structures, forward=forward)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1483, in apply_recipe
    struct.remove_van_der_waals_bonds()
  File "rmgpy/molecule/molecule.py", line 1091, in rmgpy.molecule.molecule.Molecule.remove_van_der_waals_bonds
  File "rmgpy/molecule/molecule.py", line 1097, in rmgpy.molecule.molecule.Molecule.remove_van_der_waals_bonds
RuntimeError: dictionary changed

rmgpy/molecule/molecule.py

@@ -1092,11 +1092,14 @@ def remove_van_der_waals_bonds(self):
         """
         Remove all van der Waals bonds.
         """
-        cython.declare(atom=Atom, bond=Bond)
+        cython.declare(atom=Atom, bond=Bond, to_remove=list)
         for atom in self.atoms:
+            to_remove = []
             for bond in atom.edges.values():
                 if bond.is_van_der_waals():
-                    self.remove_bond(bond)
+                    to_remove.append(bond)
+            for bond in to_remove:
+                self.remove_bond(bond)
 
     def sort_atoms(self):
         """