Vd w bonds

rmgpy/data/kinetics/family.py

@@ -1670,11 +1670,17 @@ 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
 
         return False
 

rmgpy/molecule/converter.py

@@ -97,7 +97,7 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
                 label_dict[label] = [saved_index]
     rd_bonds = Chem.rdchem.BondType
     orders = {'S': rd_bonds.SINGLE, 'D': rd_bonds.DOUBLE, 'T': rd_bonds.TRIPLE, 'B': rd_bonds.AROMATIC,
-              'Q': rd_bonds.QUADRUPLE}
+              'Q': rd_bonds.QUADRUPLE, 'vdW': rd_bonds.UNSPECIFIED}
     # Add the bonds
     for atom1 in mol.vertices:
         for atom2, bond in atom1.edges.items():

rmgpy/molecule/draw.py

@@ -1214,6 +1214,9 @@ def _render_bond(self, atom1, atom2, bond, cr):
             elif bond.is_hydrogen_bond():
                 # Draw a dashed line
                 self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])
+            elif bond.is_van_der_waals():
+                # Draw a dashed line
+                self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])
             else:
                 self._draw_line(cr, x1, y1, x2, y2)
         else:

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,
@@ -1258,9 +1258,19 @@ def remove_van_der_waals_bonds(self):
         Remove all van der Waals bonds.
         """
         cython.declare(bond=Bond)
-        for bond in self.get_all_edges():
-            if bond.is_van_der_waals():
-                self.remove_bond(bond)
+        if self.is_multidentate():
+            #bond_types =
+            #possible_bonds_with_resonance =  #TODO: Include possible nitrogen bonds
+            if any([k in ['O-X', 'C#X', 'C=X', 'C-X'] for k in self.enumerate_bonds()]):
+                pass
+            else:
+                for bond in self.get_all_edges():
+                    if bond.is_van_der_waals():
+                        self.remove_bond(bond)
+        else:
+            for bond in self.get_all_edges():
+                if bond.is_van_der_waals():
+                    self.remove_bond(bond)
 
     def sort_atoms(self):
         """
@@ -2942,6 +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)