def setUpClass(cls):
"""
A method that is run before all unit tests in this class.
"""
cls.maxDiff = None
cls.rmgdb = rmgdb.make_rmg_database_object()
rmgdb.load_families_only(cls.rmgdb)
cls.rxn1 = ARCReaction(reactants=['CH4', 'OH'],
products=['CH3', 'H2O'])
cls.rxn1.rmg_reaction = Reaction(reactants=[
Species().fromSMILES(str('C')),
Species().fromSMILES(str('[OH]'))
],
products=[
Species().fromSMILES(
str('[CH3]')),
Species().fromSMILES(str('O'))
])
cls.rxn2 = ARCReaction(reactants=['C2H5', 'OH'],
products=['C2H4', 'H2O'])
cls.rxn2.rmg_reaction = Reaction(reactants=[
Species().fromSMILES(str('C[CH2]')),
Species().fromSMILES(str('[OH]'))
],
products=[
Species().fromSMILES(str('C=C')),
Species().fromSMILES(str('O'))
])
cls.rxn3 = ARCReaction(reactants=['CH3CH2NH'], products=['CH2CH2NH2'])
cls.rxn3.rmg_reaction = Reaction(
reactants=[Species().fromSMILES(str('CC[NH]'))],
products=[Species().fromSMILES(str('[CH2]CN'))])
def test_determine_family(self):
"""Test the determine_family() function."""
rxn = ARCReaction(r_species=[ARCSpecies(label='CH2CH2CH3', smiles='[CH2]CC')],
p_species=[ARCSpecies(label='CH3CHCH3', smiles='C[CH]C')])
self.assertIsNone(rxn.family)
rmgdb.determine_family(rxn, db=None)
self.assertEqual(rxn.family.label, 'intra_H_migration')
rxn = ARCReaction(r_species=[ARCSpecies(label='C2H6', smiles='CC'),
ARCSpecies(label='OH', smiles='[OH]')],
p_species=[ARCSpecies(label='water', smiles='O'),
ARCSpecies(label='C2H5', smiles='[CH2]C')])
self.assertIsNone(rxn.family)
rmgdb.determine_family(rxn, db=self.rmgdb)
self.assertEqual(rxn.family.label, 'H_Abstraction')
r_1 = ARCSpecies(label='C3H6O', smiles='CCC=O')
r_2 = ARCSpecies(label='C4H9O', smiles='[CH2]C(C)CO')
p_1 = ARCSpecies(label='C3H5O', smiles='CC=C[O]') # This is the "wrong" resonance structure on purpose.
p_2 = ARCSpecies(label='C4H10O', smiles='CC(C)CO')
rxn = ARCReaction(reactants=['C3H6O', 'C4H9O'], products=['C3H5O', 'C4H10O'],
r_species=[r_1, r_2], p_species=[p_1, p_2])
self.assertIsNone(rxn.family)
rmgdb.determine_family(rxn, db=self.rmgdb)
self.assertEqual(rxn.family.label, 'H_Abstraction')
def test_rmg_reaction_to_str(self):
"""Test the rmg_reaction_to_str() method and the reaction label generated"""
spc1 = Species().fromSMILES(str('CON=O'))
spc1.label = str('CONO')
spc2 = Species().fromSMILES(str('C[N+](=O)[O-]'))
spc2.label = str('CNO2')
rmg_reaction = Reaction(reactants=[spc1], products=[spc2])
rxn = ARCReaction(rmg_reaction=rmg_reaction)
rxn_str = rxn.rmg_reaction_to_str()
self.assertEqual(rxn_str, 'CON=O <=> [O-][N+](=O)C')
self.assertEqual(rxn.label, 'CONO <=> CNO2')
def test_from_dict(self):
"""Test Species.from_dict()"""
rxn_dict = self.rxn1.as_dict()
rxn = ARCReaction(reaction_dict=rxn_dict)
self.assertEqual(rxn.label, 'CH4 + OH <=> CH3 + H2O')
self.assertEqual(rxn.ts_methods,
[tsm.lower() for tsm in default_ts_methods])