simplify auto cut algorithm

Author: donerancl

rmgpy/rmg/model.py

@@ -303,18 +303,17 @@ def make_new_species(self, object, label="", reactive=True, check_existing=True,
 
         # If we're here then we're ready to make the new species
         if check_cut:
-            #set size_threshold to about half the molecule size
+            # set size_threshold to about half the molecule size
             size_threshold = int((molecule.smiles.count("C")+molecule.smiles.count("c"))/2)
-            #try to cut_molecule with size threshold set above, if error, try with default size_threshold
-            try: 
-                mols = molecule.cut_molecule(cut_through=False,size_threshold=size_threshold)
-            except:
-                try:
-                    mols = molecule.cut_molecule(cut_through=False)
-                except AttributeError:
-                        # it's Molecule object, change it to Fragment and then cut
-                        molecule = Fragment().from_adjacency_list(molecule.to_adjacency_list())
-                        mols = molecule.cut_molecule(cut_through=False)
+            # if the molecule type is Molecule, change type to Fragment before cutting
+            if type(molecule) == Molecule:
+                molecule = Fragment().from_adjacency_list(molecule.to_adjacency_list())
+            # try to cut_molecule with size threshold set above
+            mols = molecule.cut_molecule(cut_through=False,size_threshold=size_threshold)
+            # if cut above can't be made try with default size_threshold = 5
+            if len(mols) == 1:
+                mols = molecule.cut_molecule(cut_through=False)
+            # if cut above can't be made, don't cut
             if len(mols) == 1:
                 molecule = mols[0]
             else: