change is_molecule_forbidden

Author: bjkreitz

rmgpy/data/kinetics/family.py

@@ -1670,11 +1670,22 @@ def is_molecule_forbidden(self, molecule):
             return True
 
         # forbid vdw multi-dentate molecules for surface families
+        surface_sites = []
         if "surface" in self.label.lower():
-            if molecule.get_num_atoms('X') > 1:
-                for atom in molecule.atoms:
-                    if atom.atomtype.label == 'Xv':
-                        return True
+            if "surface_monodentate_to_vdw_bidentate" in self.label.lower() and molecule.get_num_atoms('X') > 1:
+                surface_sites = [atom.atomtype.label for atom in molecule.atoms if 'X' in atom.atomtype.label]
+                if all(site == 'Xv' for site in surface_sites):
+                    return True
+            else:
+                if molecule.get_num_atoms('X') > 1:
+                    for atom in molecule.atoms:
+                        if atom.atomtype.label == 'Xv':
+                            return True
+      #  elif "surface" in self.label.lower():
+      #      if molecule.get_num_atoms('X') > 1:
+      #          for atom in molecule.atoms:
+      #              if atom.atomtype.label == 'Xv':
+      #                  return True
 
         return False
 

rmgpy/molecule/molecule.py

@@ -62,7 +62,7 @@
 
 ################################################################################
 
-bond_orders = {'S': 1, 'D': 2, 'T': 3, 'B': 1.5}
+bond_orders = {'S': 1, 'D': 2, 'T': 3, 'B': 1.5, 'vdW': 0}
 
 globals().update({
     'bond_orders': bond_orders,
@@ -2952,6 +2952,8 @@ def get_desorbed_molecules(self):
                     bonded_atom.increment_radical()
                     bonded_atom.increment_lone_pairs()
                     bonded_atom.label = '*4'
+                elif bond.is_van_der_waals():
+                    bonded_atom.label = '*5'
                 else:
                     raise NotImplementedError("Can't remove surface bond of type {}".format(bond.order))
             desorbed_molecule.remove_atom(site)