Rename and simplify species_to_dict

Author: rwest

rmgpy/yaml_cantera.py

@@ -230,7 +230,7 @@ def get_mech_dict_surface(spcs, rxns, solvent="solvent", solvent_data=None):
             names[i] += "-" + str(names.count(name))
 
     result_dict = dict()
-    result_dict["species"] = [species_to_dict(x, spcs, names=names) for x in spcs]
+    result_dict["species"] = [species_to_dict(x) for x in spcs]
 
     # separate gas and surface reactions
 
@@ -258,7 +258,7 @@ def get_mech_dict_nonsurface(spcs, rxns, solvent="solvent", solvent_data=None):
             names[i] += "-" + str(names.count(name))
 
     result_dict = dict()
-    result_dict["species"] = [species_to_dict(x, spcs, names=names) for x in spcs]
+    result_dict["species"] = [species_to_dict(x) for x in spcs]
 
     reactions = []
     for rmg_rxn in rxns:
@@ -299,32 +299,36 @@ def reaction_to_dicts(obj, spcs):
     return reaction_list
 
 
-def species_to_dict(obj, spc, names=None, label="solvent"):
+def species_to_dict(species):
     """
-    Takes an RMG species object (obj), returns a list of dictionaries
+    Takes an RMG species object, returns a list of dictionaries
     for YAML properties. Also adds in the number of surface sites
     ('sites') to dictionary.
     """
-
-    result_dict = dict()
-
-    if isinstance(obj, Species):
-        s = obj.to_cantera(use_chemkin_identifier=True)
-        species_data = s.input_data
-        try:
-            result_dict["note"] = obj.transport_data.comment
-        except:
-            pass
-        if "size" in species_data:
-            sites = species_data["size"]
-            species_data.pop("size", None)
-            species_data["sites"] = sites
-        species_data.update(result_dict)
-        return (
-            species_data  # returns composition, name, thermo, and transport, and note
-        )
-    else:
-        raise Exception("Species object must be an RMG Species object")
+    if not isinstance(species, Species):
+        raise TypeError("species object must be an RMG Species")
+
+    cantera_species = species.to_cantera(use_chemkin_identifier=True)
+    species_data = cantera_species.input_data
+
+    # if species.transport_data.comment exists, add it to species_data["note"]
+    try:
+        transport_comment = species.transport_data.comment
+        if transport_comment:
+            if "note" in species_data:
+                species_data["note"] += f" Transport data: {transport_comment}"
+            else:
+                species_data["note"] = f"Transport data: {transport_comment}"
+    except AttributeError:
+        pass
+
+    if "size" in species_data:
+        sites = species_data["size"]
+        species_data.pop("size", None)
+        species_data["sites"] = sites
+
+     # returns composition, name, thermo, and transport, and note
+    return species_data
 
 
 class CanteraWriter(object):