class TestReact(unittest.TestCase):
def setUp(self):
"""
A function run before each unit test in this class.
"""
# load kinetics database
db_path = settings['database.directory']
self.database = RMGDatabase()
# forbidden structure loading
self.database.loadForbiddenStructures(
os.path.join(db_path, 'forbiddenStructures.py'))
# kinetics family loading
self.database.loadKinetics(os.path.join(db_path, 'kinetics'),
kineticsFamilies=[
'R_Recombination', 'H_Abstraction',
'1,2_Insertion_carbene'
],
reactionLibraries=[])
def test_react_fragments1(self):
frag1 = afm.fragment.Fragment(
label='frag1').from_SMILES_like_string('c1ccccc1CCCR')
fragment_tuple = (frag1, )
reactions = afm.react.react_fragments(
self.database.kinetics,
fragment_tuple,
only_families=['R_Recombination'],
prod_resonance=False)
self.assertTrue(len(reactions) == 28)
def test_react_fragments2(self):
frag1 = afm.fragment.Fragment(
label='frag1').from_SMILES_like_string('c1ccccc1CCCR')
frag2 = afm.fragment.Fragment(
label='frag2').from_SMILES_like_string('[CH2]CR')
fragment_tuple = (frag1, frag2)
reactions = afm.react.react_fragments(self.database.kinetics,
fragment_tuple,
only_families=['H_Abstraction'],
prod_resonance=False)
self.assertTrue(len(reactions) == 11)
def test_generate_reactions_from_families1(self):
frag1 = afm.fragment.Fragment(
label='frag1').from_SMILES_like_string('CC')
spec1 = Species(molecule=[frag1])
spec_tuple = (spec1, )
reactions = self.database.kinetics.generate_reactions_from_families(
spec_tuple)
self.assertTrue(len(reactions) == 3)
def test_generate_reactions_from_families2(self):
frag1 = afm.fragment.Fragment(
label='frag1').from_SMILES_like_string('CCR')
spec1 = Species(molecule=[frag1])
spec_tuple = (spec1, )
reactions = self.database.kinetics.generate_reactions_from_families(
spec_tuple)
self.assertTrue(len(reactions) == 4)
