Added comments for Boron BDE data and deleted a temporary workaround.

rmgpy/molecule/element.py

@@ -341,7 +341,9 @@ def get_element(value, isotope=-1):
 # (between RT and 3/2 RT), and this difference is usually much smaller than the uncertainty in the bond dissociation
 # energy itself. Therefore, the discrepancy between 0 K and 298 K shouldn't matter too much.
 # But for any new entries, try to use the consistent reference state of 298 K.
-bde_elements = ['C', 'N', 'H', 'O', 'S', 'Cl', 'Si', 'P', 'F', 'Br', 'I', 'B']  # elements supported by BDE
+# Boron BDE data were from the NBS/NIST data, but B-C and B-Si are values at 0 K. 
+bde_elements = ['C', 'N', 'H', 'O', 'S', 'Cl', 'Si', 'P', 'F', 'Br', 'I', 'B']  
+# elements supported by BDE
 bde_dict = {('H', 'H', 1.0): (432.0, 'kJ/mol'), ('H', 'C', 1): (411.0, 'kJ/mol'),
             ('H', 'N', 1): (386.0, 'kJ/mol'), ('H', 'O', 1.0): (459.0, 'kJ/mol'),
             ('H', 'P', 1): (322.0, 'kJ/mol'), ('H', 'S', 1): (363.0, 'kJ/mol'),

rmgpy/rmg/reactors.py

@@ -582,10 +582,6 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             except AttributeError:
                 # means it is fragment's cutting label
                 pass
-        # TEMPORARY hack. Turn boron into carbon
-        # atomnums[6] = atomnums.get(5,0) + atomnums.get(6,0)
-        # if 5 in atomnums: 
-        #     del atomnums[5]
         bondnum = len(obj.molecule[0].get_all_edges())
         if not obj.molecule[0].contains_surface_site():
             rad = rms.getspeciesradius(atomnums, bondnum)