def test_initial_species(self):
"""Test we can check whether the solvent is listed as one of the initial species in various scenarios"""
# Case 1. when SMILES for solvent is available, the molecular structures of the initial species and the solvent
# are compared to check whether the solvent is in the initial species list
# Case 1-1: the solvent water is not in the initialSpecies list, so it raises Exception
rmg = RMG()
rmg.initial_species = []
solute = Species(label='n-octane', molecule=[Molecule().from_smiles('C(CCCCC)CC')])
rmg.initial_species.append(solute)
rmg.solvent = 'water'
solvent_structure = Species().from_smiles('O')
self.assertRaises(Exception, self.database.check_solvent_in_initial_species, rmg, solvent_structure)
# Case 1-2: the solvent is now octane and it is listed as the initialSpecies. Although the string
# names of the solute and the solvent are different, because the solvent SMILES is provided,
# it can identify the 'n-octane' as the solvent
rmg.solvent = 'octane'
solvent_structure = Species().from_smiles('CCCCCCCC')
self.database.check_solvent_in_initial_species(rmg, solvent_structure)
self.assertTrue(rmg.initial_species[0].is_solvent)
# Case 2: the solvent SMILES is not provided. In this case, it can identify the species as the
# solvent by looking at the string name.
# Case 2-1: Since 'n-octane and 'octane' are not equal, it raises Exception
solvent_structure = None
self.assertRaises(Exception, self.database.check_solvent_in_initial_species, rmg, solvent_structure)
# Case 2-2: The label 'n-ocatne' is corrected to 'octane', so it is identified as the solvent
rmg.initial_species[0].label = 'octane'
self.database.check_solvent_in_initial_species(rmg, solvent_structure)
self.assertTrue(rmg.initial_species[0].is_solvent)
