def test_instantiate_reference_species(self):
"""
Test that a ReferenceSpecies object can be instantiated with the minimal acceptable input, and throws an error
if the minimal acceptable input is not given.
"""
ref_spcs = ReferenceSpecies(species=self.ethane)
self.assertEqual(ref_spcs.smiles, 'CC')
self.assertEqual(ref_spcs.inchi_key,
self.ethane.molecule[0].to_inchi_key())
ref_from_smiles = ReferenceSpecies(smiles='CCC')
self.assertEqual(ref_from_smiles.smiles, 'CCC')
self.assertEqual(ref_from_smiles.inchi_key,
self.propane.molecule[0].to_inchi_key())
ref_from_inchi = ReferenceSpecies(inchi='InChI=1S/C2H6/c1-2/h1-2H3')
self.assertEqual(ref_from_inchi.smiles, 'CC')
self.assertEqual(ref_from_inchi.inchi_key,
self.ethane.molecule[0].to_inchi_key())
ref_from_adj = ReferenceSpecies(
adjacency_list=
'1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}\n2 H u0 p0 c0 {1,S}\n'
'3 H u0 p0 c0 {1,S}\n4 H u0 p0 c0 {1,S}\n5 H u0 p0 c0 {1,S}\n')
self.assertEqual(ref_from_adj.smiles, 'C')
self.assertEqual(ref_from_adj.inchi_key,
self.methane.molecule[0].to_inchi_key())
with self.assertRaises(ValueError):
ReferenceSpecies()
def test_save_ref_to_yaml(self):
"""
Test that a ReferenceSpecies object can be saved to a YAML file successfully
"""
label = 'test_reference_species'
ref_spcs = ReferenceSpecies(species=self.ethane, label=label)
self.assertEqual(ref_spcs.label, label)
ref_spcs.save_yaml(path=SPECIES_DIR)
loaded_ref = ReferenceSpecies.__new__(ReferenceSpecies)
load_path = os.path.join(SPECIES_DIR, f'{label}.yml')
loaded_ref.load_yaml(path=load_path)
self.assertEqual(loaded_ref.smiles, 'CC')
# Finally, delete this newly created file
os.remove(load_path)
def load_ref_from_yaml(self):
"""
Test that the example ReferenceSpecies YAML file can be loaded
"""
ref_spcs = ReferenceSpecies.__new__(ReferenceSpecies)
ref_spcs.load_yaml(os.path.join(SPECIES_DIR, 'reference_species_example.yml'))
self.assertEqual(ref_spcs.smiles, 'C#C[CH2]')
self.assertEqual(ref_spcs.label, 'example_reference_species')
self.assertIsInstance(ref_spcs.calculated_data, CalculatedDataEntry)
def test_extract_level_of_theory(self):
"""
Test that a given level of theory can be extracted from the reference set database
"""
# Create a quick example database
ref_data_1 = ReferenceDataEntry(ThermoData(H298=(100, 'kJ/mol', '+|-', 2)))
ref_data_2 = ReferenceDataEntry(ThermoData(H298=(25, 'kcal/mol', '+|-', 1)))
calc_data_1 = CalculatedDataEntry(ThermoData(H298=(110, 'kJ/mol')))
calc_data_2 = CalculatedDataEntry(ThermoData(H298=(120, 'kJ/mol')))
ethane = ReferenceSpecies(smiles='CC',
reference_data={'precise': ref_data_1, 'less_precise': ref_data_2},
calculated_data={LevelOfTheory('good_chem'): calc_data_1,
LevelOfTheory('bad_chem'): calc_data_2},
preferred_reference='less_precise')
propane = ReferenceSpecies(smiles='CCC',
reference_data={'precise': ref_data_1, 'less_precise': ref_data_2},
calculated_data={LevelOfTheory('good_chem'): calc_data_1,
LevelOfTheory('bad_chem'): calc_data_2})
butane = ReferenceSpecies(smiles='CCCC',
reference_data={'precise': ref_data_1, 'less_precise': ref_data_2},
calculated_data={LevelOfTheory('bad_chem'): calc_data_2})
database = ReferenceDatabase()
database.reference_sets = {'testing_1': [ethane, butane], 'testing_2': [propane]}
model_chem_list = database.extract_level_of_theory(LevelOfTheory('good_chem'))
self.assertEqual(len(model_chem_list), 2)
self.assertIsInstance(model_chem_list[0], ErrorCancelingSpecies)
for spcs in model_chem_list:
smiles = spcs.molecule.to_smiles()
self.assertNotIn(smiles, ['CCCC'])
self.assertIn(smiles, ['CC', 'CCC'])
if smiles == 'CC': # Test that `less_precise` is the source since it was set manually as preferred
self.assertAlmostEqual(spcs.high_level_hf298.value_si, 25.0*4184.0)
if smiles == 'CCC': # Test that `precise` is the source since it has the lowest uncertainty
self.assertAlmostEqual(spcs.high_level_hf298.value_si, 100.0*1000.0)