use molecule.smiles instead of molecule.to_smiles() in yaml writer

This should speed up execution time by accessing the property each time instead of regenerating it, see : ReactionMechanismGenerator#2499 (comment)

rmgpy/yml.py

@@ -99,7 +99,7 @@ def get_mech_dict(spcs, rxns, solvent='solvent', solvent_data=None):
 
 
 def get_radicals(spc):
- if spc.molecule[0].to_smiles() == "[O][O]": # treat oxygen as stable to improve radical analysis
+ if spc.molecule[0].smiles == "[O][O]": # treat oxygen as stable to improve radical analysis
  return 0
  else:
  return spc.molecule[0].multiplicity-1
@@ -112,7 +112,7 @@ def obj_to_dict(obj, spcs, names=None, label="solvent"):
  result_dict["type"] = "Species"
  if obj.contains_surface_site():
  result_dict["adjlist"] = obj.molecule[0].to_adjacency_list()
- result_dict["smiles"] = obj.molecule[0].to_smiles()
+ result_dict["smiles"] = obj.molecule[0].smiles
  result_dict["thermo"] = obj_to_dict(obj.thermo, spcs)
  result_dict["radicalelectrons"] = get_radicals(obj)
  if obj.liquid_volumetric_mass_transfer_coefficient_data:

test/rmgpy/rmg/inputTest.py

@@ -93,6 +93,19 @@ def test_importing_database_reaction_libraries_from_true_tuple(self):
  assert rmg.reaction_libraries[0][1]
 
 
+class TestRMSYAMLWriterDisable(unittest.TestCase):
+ """
+ Default behavior of RMG is to enable so test ability to disable
+ """
+
+ def test_disable_rms_yaml_writer(self):
+ """
+ generateRMSEachIter = False in input should set the corresponding property in RMG instance
+ """
+ global rmg
+ self.assertFalse(rmg.generate_rms_each_iter)
+
+
 class TestInputMLEstimator:
  """
  Contains unit tests rmgpy.rmg.input.mlEstimator