Merge pull request #1773 from ReactionMechanismGenerator/fix_solvaion…

…_radical_bug

Fix solvaion radical bug

rmgpy/data/solvation.py

@@ -798,8 +798,8 @@ def remove_h_bonding(self, saturated_struct, added_to_radicals, added_to_pairs,
         for atom in saturated_struct.atoms:
             # Iterate over heavy (non-hydrogen) atoms
             if atom.is_non_hydrogen() and atom.radical_electrons > 0:
-                for electron in range(1, atom.radical_electrons):
-                    # Get solute data for radical group    
+                for electron in range(atom.radical_electrons):
+                    # Get solute data for radical group
                     try:
                         self._add_group_solute_data(solute_data, self.groups['radical'], saturated_struct, {'*': atom})
                     except KeyError:

rmgpy/data/solvationTest.py

@@ -193,6 +193,22 @@ def test_radical_and_lone_pair_generation(self):
         solute_data = self.database.get_solute_data_from_groups(species)
         self.assertIsNotNone(solute_data)
 
+    def test_radical_solute_group(self):
+        """Test that the existing radical group is found for the radical species when using group additivity"""
+        # First check whether the radical group is found for the radical species
+        rad_species = Species(smiles='[OH]')
+        rad_solute_data = self.database.get_solute_data_from_groups(rad_species)
+        self.assertTrue('radical' in rad_solute_data.comment)
+        # Then check that the radical and its saturated species give different solvation free energies
+        saturated_struct = rad_species.molecule[0].copy(deep=True)
+        saturated_struct.saturate_radicals()
+        sat_species = Species(molecule=[saturated_struct])
+        sat_solute_data = self.database.get_solute_data_from_groups(sat_species)
+        solvent_data = self.database.get_solvent_data('water')
+        rad_solvation_correction = self.database.get_solvation_correction(rad_solute_data, solvent_data)
+        sat_solvation_correction = self.database.get_solvation_correction(sat_solute_data, solvent_data)
+        self.assertNotAlmostEqual(rad_solvation_correction.gibbs / 1000, sat_solvation_correction.gibbs / 1000)
+
     def test_correction_generation(self):
         """Test we can estimate solvation thermochemistry."""
         self.testCases = [