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fixed the solvation GAV heuristic #1832

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Dec 3, 2019
Merged

fixed the solvation GAV heuristic #1832

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29e5ff4
fixed the solvation GAV heuristic
yunsiechung Nov 26, 2019
55eb6b3
simplified the existing solvation unit test
yunsiechung Nov 27, 2019
cbf446f
unit test for solute GAV with resonance structures
yunsiechung Nov 27, 2019
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34 changes: 8 additions & 26 deletions rmgpy/data/solvation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -702,32 +702,14 @@ def get_solute_data_from_groups(self, species):
additivity method. If no group additivity values are loaded, a
:class:`DatabaseError` is raised.

It averages (linearly) over the desciptors for each Molecule (resonance isomer)
in the Species.
"""
solute_data = SoluteData(0.0, 0.0, 0.0, 0.0, 0.0)
count = 0
comments = []
for molecule in species.molecule:
molecule.clear_labeled_atoms()
molecule.update_atomtypes()
sdata = self.estimate_solute_via_group_additivity(molecule)
solute_data.S += sdata.S
solute_data.B += sdata.B
solute_data.E += sdata.E
solute_data.L += sdata.L
solute_data.A += sdata.A
count += 1
comments.append(sdata.comment)

solute_data.S /= count
solute_data.B /= count
solute_data.E /= count
solute_data.L /= count
solute_data.A /= count

# Print groups that are used for debugging purposes
solute_data.comment = "Average of {0}".format(" and ".join(comments))
It estimates the solute data for the first item in the species's
molecule list because it is the most stable resonance structure found
by gas-phase thermo estimate.
"""
molecule = species.molecule[0]
molecule.clear_labeled_atoms()
molecule.update_atomtypes()
solute_data = self.estimate_solute_via_group_additivity(molecule)

return solute_data

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26 changes: 24 additions & 2 deletions rmgpy/data/solvationTest.py
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Expand Up @@ -112,14 +112,36 @@ def test_solute_generation(self):
]

for name, smiles, S, B, E, L, A, V in self.testCases:
species = Species(molecule=[Molecule(smiles=smiles)])
solute_data = self.database.get_solute_data_from_groups(Species(molecule=[species.molecule[0]]))
species = Species(smiles=smiles)
solute_data = self.database.get_solute_data_from_groups(species)
self.assertAlmostEqual(solute_data.S, S, places=2)
self.assertAlmostEqual(solute_data.B, B, places=2)
self.assertAlmostEqual(solute_data.E, E, places=2)
self.assertAlmostEqual(solute_data.L, L, places=2)
self.assertAlmostEqual(solute_data.A, A, places=2)

def test_solute_with_resonance_structures(self):
"""
Test we can estimate Abraham solute parameters correctly using group contributions
for the solute species with resonance structures.
"""
smiles = "CC1=CC=CC=C1N"
species = Species(smiles=smiles)
species.generate_resonance_structures()
solute_data = self.database.get_solute_data(species)
solvent_data = self.database.get_solvent_data('water')
solvation_correction = self.database.get_solvation_correction(solute_data, solvent_data)
dGsolv_spc = solvation_correction.gibbs / 1000
for mol in species.molecule:
spc = Species(molecule=[mol])
solute_data = self.database.get_solute_data_from_groups(spc)
solvation_correction = self.database.get_solvation_correction(solute_data, solvent_data)
dGsolv_mol = solvation_correction.gibbs / 1000
if mol == species.molecule[0]:
self.assertEqual(dGsolv_spc, dGsolv_mol)
else:
self.assertNotAlmostEqual(dGsolv_spc, dGsolv_mol)

def test_lone_pair_solute_generation(self):
"""Test we can obtain solute parameters via group additivity for a molecule with lone pairs"""
molecule = Molecule().from_adjacency_list(
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