updated filtration.py and family.py so that new kinetic families work…

… for PFAS chemistry.

rmgpy/data/kinetics/family.py

@@ -1564,7 +1564,7 @@ def apply_recipe(self, reactant_structures, forward=True, unique=True, relabel_a
                 struct.reset_ring_membership()
                 if label in ['1,2_insertion_co', 'r_addition_com', 'co_disproportionation',
                              'intra_no2_ono_conversion', 'lone_electron_pair_bond',
-                             '1,2_nh3_elimination', '1,3_nh3_elimination', 'co2_elimination_from_lactone_ether']:
+                             '1,2_nh3_elimination', '1,3_nh3_elimination', 'co2_elimination_from_lactone_ether']: #, 'enol_ether_formation']:
                     struct.update_charge()
             else:
                 raise TypeError('Expecting Molecule or Group object, not {0}'.format(struct.__class__.__name__))
@@ -1669,8 +1669,9 @@ def _generate_product_structures(self, reactant_structures, maps, forward, relab
             product_structures = self.apply_recipe(reactant_structures, forward=forward, relabel_atoms=relabel_atoms)
             if not product_structures:
                 return None
-        except (InvalidActionError, KekulizationError, AtomTypeError): #added in by NK
+        except (InvalidActionError, KekulizationError, AtomTypeError) as e: #added in by NK
             # If unable to apply the reaction recipe, then return no product structures
+            print(e)
             return None
         except ActionError:
             logging.error('Could not generate product structures for reaction family {0} in {1} '

rmgpy/molecule/filtration.py

@@ -64,6 +64,8 @@ def filter_structures(mol_list, mark_unreactive=True, allow_expanded_octet=True,
     if not all([(mol.multiplicity == mol_list[0].multiplicity) for mol in mol_list]):
         raise ValueError("Cannot filter structures with different multiplicities!")
 
+    if 'F' in mol_list[0].smiles: 
+        print('testing')
     # Get an octet deviation list
     octet_deviation_list = get_octet_deviation_list(mol_list, allow_expanded_octet=allow_expanded_octet)
 
@@ -117,7 +119,18 @@ def get_octet_deviation(mol, allow_expanded_octet=True):
             continue
         val_electrons = 2 * (int(atom.get_total_bond_order()) + atom.lone_pairs) + atom.radical_electrons
         if atom.is_carbon() or atom.is_nitrogen() or atom.is_oxygen():
+            if '(F)[C]OC(F)' in mol.smiles: #we need to have an exception for some PFAS chemistry 
+                # There are some cases for PFAS chemistry where a resonance structure of molecules like FC(F)(F)[C]OC(F)(F)F is FC(F)(F)[C-]=[O+]C(F)(F)F. 
+                # However, the get_octet_deviation function marks the FC(F)(F)[C]OC(F)(F)F as unreactive and keeps the FC(F)(F)[C-]=[O+]C(F)(F)F as reactive. 
+                # This is a problem because Brown University calculated reaction rates using the first structure, so we want to keep that reactive and write a reaction recipe with this structure. 
+                if atom.is_carbon() and val_electrons==6: #this is the C with just 2 single bonds and no unpaired
+                    val_electrons += 2 #add two to the valence charge so we get a total octet deviation of 0
+                if atom.is_oxygen():
+                    pass #no modification of oxygen valence 
+            else: 
+                pass  # if not related to PFAS chemistry
             octet_deviation += abs(8 - val_electrons)  # expecting C/N/O to be near octet
+
         elif atom.is_sulfur():
             if not allow_expanded_octet:
                 # If allow_expanded_octet is False, then adhere to the octet rule for sulfur as well.