def extract_dataset(ref_database: ReferenceDatabase, model_chemistry: str) -> BACDataset:
"""
Extract species for a given model chemistry from a reference
database and convert to a BACDataset.
Args:
ref_database: Reference database
model_chemistry: Model chemistry.
Returns:
BACDataset containing species with data available at given model chemistry.
"""
species = ref_database.extract_model_chemistry(model_chemistry, as_error_canceling_species=False)
return BACDataset([BACDatapoint(spc, model_chemistry=model_chemistry) for spc in species])
def test_extract_model_chemistry(self):
"""
Test that a given model chemistry 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={
'good_chem': calc_data_1,
'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={
'good_chem': calc_data_1,
'bad_chem': calc_data_2
})
butane = ReferenceSpecies(smiles='CCCC',
reference_data={
'precise': ref_data_1,
'less_precise': ref_data_2
},
calculated_data={'bad_chem': calc_data_2})
database = ReferenceDatabase()
database.reference_sets = {
'testing_1': [ethane, butane],
'testing_2': [propane]
}
model_chem_list = database.extract_model_chemistry('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)