Changed constraint for max carbene radicals to be 1, added a new exce…

…ption to atomtype because it was causing an error for 1,2+Cycloaddition, and had some issues with charges in CO2 so had to append hardcoded families in family.py to include 'co2_elimination_from_lactone_ether'

rmgpy/constraints.py

@@ -128,7 +128,7 @@ def fails_species_constraints(species):
         if struct.get_singlet_carbene_count() > max_carbenes:
             return True
 
-    max_carbene_radicals = species_constraints.get('maximumCarbeneRadicals', 0)
+    max_carbene_radicals = species_constraints.get('maximumCarbeneRadicals', 1) #changing this from 0 to 1 (PFAS chemistry involves carbene radicals)
     if max_carbene_radicals != -1:
         if struct.get_singlet_carbene_count() > 0 and struct.get_radical_count() > max_carbene_radicals:
             return True

rmgpy/data/kinetics/family.py

@@ -1384,8 +1384,8 @@ def apply_recipe(self, reactant_structures, forward=True, unique=True, relabel_a
         will be reversed to assist in identifying forbidden structures.
         """
         #added in by NK
-        print(reactant_structures)
-        logging.info(reactant_structures)
+        #print(reactant_structures)
+        #logging.info(reactant_structures)
 
         # There is some hardcoding of reaction families in this function, so
         # we need the label of the reaction family for this
@@ -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']:
+                             '1,2_nh3_elimination', '1,3_nh3_elimination', 'co2_elimination_from_lactone_ether']:
                     struct.update_charge()
             else:
                 raise TypeError('Expecting Molecule or Group object, not {0}'.format(struct.__class__.__name__))

rmgpy/molecule/atomtype.py

@@ -284,6 +284,22 @@ def get_features(self):
     'I','I1s',
     'F','F1s'])
 
+
+ATOMTYPES['R!O']  = AtomType(label='R!O', generic=['R'], specific=[
+    'Val4','Val5','Val6','Val7',
+    'He','Ne','Ar',
+    'C','Ca','Cs','Csc','Cd','CO','CS','Cdd','Cdc','Ctc','Ct','Cb','Cbf','Cq','C2s','C2sc','C2d','C2dc','C2tc',
+    'N','N0sc','N1s','N1sc','N1dc','N3s','N3sc','N3d','N3t','N3b','N5sc','N5dc','N5ddc','N5dddc','N5tc','N5b','N5bd',
+    'H',
+    'Si','Sis','Sid','Sidd','Sit','SiO','Sib','Sibf','Siq',
+    'P','P0sc','P1s','P1sc','P1dc','P3s','P3d','P3t','P3b','P5s','P5sc','P5d','P5dd','P5dc','P5ddc','P5t','P5td','P5tc','P5b','P5bd',
+    'S','Sa','S0sc','S2s','S2sc','S2d','S2dc','S2tc','S4s','S4sc','S4d','S4dd','S4dc','S4b','S4t','S4tdc','S6s','S6sc','S6d','S6dd','S6ddd','S6dc','S6t','S6td','S6tt','S6tdc',
+    'Cl','Cl1s',
+    'Br','Br1s',
+    'I','I1s',
+    'F','F1s'])
+
+
 ATOMTYPES['R!H!Val7']  = AtomType(label='R!H!Val7', generic=['R'], specific=[
     'Val4','Val5','Val6',
     'He','Ne','Ar',
@@ -640,6 +656,9 @@ def get_features(self):
 
 ATOMTYPES['R'].set_actions(increment_bond=['R'], decrement_bond=['R'], form_bond=['R'], break_bond=['R'], increment_radical=['R'], decrement_radical=['R'], increment_lone_pair=['R'], decrement_lone_pair=['R'])
 ATOMTYPES['R!H'].set_actions(increment_bond=['R!H'], decrement_bond=['R!H'], form_bond=['R!H'], break_bond=['R!H'], increment_radical=['R!H'], decrement_radical=['R!H'], increment_lone_pair=['R!H'], decrement_lone_pair=['R!H'])
+
+ATOMTYPES['R!O'].set_actions(increment_bond=['R!O'], decrement_bond=['R!O'], form_bond=['R!O'], break_bond=['R!O'], increment_radical=['R!O'], decrement_radical=['R!O'], increment_lone_pair=['R!O'], decrement_lone_pair=['R!O'])
+
 ATOMTYPES['R!H!Val7'].set_actions(increment_bond=['R!H!Val7'], decrement_bond=['R!H!Val7'], form_bond=['R!H!Val7'], break_bond=['R!H!Val7'], increment_radical=['R!H!Val7'], decrement_radical=['R!H!Val7'], increment_lone_pair=['R!H!Val7'], decrement_lone_pair=['R!H!Val7'])
 ATOMTYPES['Val4'].set_actions(increment_bond=['Val4'], decrement_bond=['Val4'], form_bond=['Val4'], break_bond=['Val4'], increment_radical=['Val4'], decrement_radical=['Val4'], increment_lone_pair=['Val4'], decrement_lone_pair=['Val4'])
 ATOMTYPES['Val5'].set_actions(increment_bond=['Val5'], decrement_bond=['Val5'], form_bond=['Val5'], break_bond=['Val5'], increment_radical=['Val5'], decrement_radical=['Val5'], increment_lone_pair=['Val5'], decrement_lone_pair=['Val5'])