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Fix solvaion radical bug #1773

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merged 3 commits into from
Nov 27, 2019
Merged

Fix solvaion radical bug #1773

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0ff4d94
fixed a bug with solvation GAV not finding radical
yunsiechung Oct 18, 2019
9370237
added solvation unittest to check radical GAV
yunsiechung Oct 18, 2019
8e93013
added unittest to compare the radical and saturated
yunsiechung Nov 27, 2019
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4 changes: 2 additions & 2 deletions rmgpy/data/solvation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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16 changes: 16 additions & 0 deletions rmgpy/data/solvationTest.py
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Expand Up @@ -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)

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Just a thought, should we add a test to check if we get the same (we shouldn't) Abraham solute parameters for OH radical and water? If we get the same values then we know something is wrong.

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I could add that test. I will just add an additional test for checking whether their A parameters are different

def test_correction_generation(self):
"""Test we can estimate solvation thermochemistry."""
self.testCases = [
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