From bbe49f45018ab423aee843ea7779070060e5bddc Mon Sep 17 00:00:00 2001
From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 26 Jul 2023 14:28:41 -0400
Subject: [PATCH] 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 : https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2499#issuecomment-1629009917
---
 rmgpy/yml.py                |  4 ++--
 test/rmgpy/rmg/inputTest.py | 15 ++++++++++++++-
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/rmgpy/yml.py b/rmgpy/yml.py
index cd8b9de5b58..f4835093856 100644
--- a/rmgpy/yml.py
+++ b/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:
diff --git a/test/rmgpy/rmg/inputTest.py b/test/rmgpy/rmg/inputTest.py
index ef69ab6ade0..c435f59a586 100644
--- a/test/rmgpy/rmg/inputTest.py
+++ b/test/rmgpy/rmg/inputTest.py
@@ -93,7 +93,20 @@ def test_importing_database_reaction_libraries_from_true_tuple(self):
         assert rmg.reaction_libraries[0][1]
 
 
-class TestInputMLEstimator:
+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(unittest.TestCase):
     """
     Contains unit tests rmgpy.rmg.input.mlEstimator
     """