def test_check_for_existing_reaction_removes_duplicates_in_opposite_directions(
self):
"""
Test that check_for_existing_reaction removes duplicate reverse reactions
"""
cerm = CoreEdgeReactionModel()
# make species' objects
s1 = Species().from_smiles("[H]")
s2 = Species().from_smiles("CC")
s3 = Species().from_smiles("[H][H]")
s4 = Species().from_smiles("C[CH2]")
s1.label = 'H'
s2.label = 'CC'
s3.label = 'HH'
s4.label = 'C[CH2]'
rxn_f = TemplateReaction(reactants=[s1, s2],
products=[s3, s4],
template=['C/H3/Cs/H3', 'H_rad'],
degeneracy=6,
family='H_Abstraction',
reverse=TemplateReaction(
reactants=[s3, s4],
products=[s1, s2],
template=['H2', 'C_rad/H2/Cs/H3'],
degeneracy=2,
family='H_Abstraction'))
rxn_r = TemplateReaction(reactants=[s3, s4],
products=[s1, s2],
template=['H2', 'C_rad/H2/Cs/H3'],
degeneracy=2,
family='H_Abstraction',
reverse=TemplateReaction(
reactants=[s1, s2],
products=[s3, s4],
template=['C/H3/Cs/H3', 'H_rad'],
degeneracy=6,
family='H_Abstraction'))
rxn_f.reactants.sort()
rxn_f.products.sort()
cerm.add_reaction_to_core(rxn_f)
cerm.register_reaction(rxn_f)
reactions = cerm.search_retrieve_reactions(rxn_r)
self.assertEqual(
1, len(reactions),
'cerm.search_retrieve_reactions could not identify reverse reaction'
)
found, rxn = cerm.check_for_existing_reaction(rxn_r)
self.assertTrue(
found,
'check_for_existing_reaction failed to identify existing reaction in the reverse direction'
)
self.assertEqual(rxn, rxn_f)
def test_check_for_existing_reaction_eliminates_identical_reactions_without_duplicate_flag(
self):
"""
Test that check_for_existing_reaction eliminates reactions with different templates and duplicate=false
"""
cerm = CoreEdgeReactionModel()
# make species' objects
spcA = Species().from_smiles('[H]')
spcB = Species().from_smiles('C=C[CH2]C')
spcC = Species().from_smiles('C=C=CC')
spcD = Species().from_smiles('[H][H]')
spcA.label = '[H]'
spcB.label = 'C=C[CH2]C'
spcC.label = 'C=C=CC'
spcD.label = '[H][H]'
spcB.generate_resonance_structures()
cerm.add_species_to_core(spcA)
cerm.add_species_to_core(spcB)
cerm.add_species_to_core(spcC)
cerm.add_species_to_core(spcD)
reaction_in_model = TemplateReaction(reactants=[spcA, spcB],
products=[spcC, spcD],
family='H_Abstraction',
template=['Csd', 'H'],
duplicate=False)
reaction_in_model.reactants.sort()
reaction_in_model.products.sort()
reaction_to_add = TemplateReaction(reactants=[spcA, spcB],
products=[spcC, spcD],
family='H_Abstraction',
template=['Cs12345', 'H'],
duplicate=False)
cerm.add_reaction_to_core(reaction_in_model)
cerm.register_reaction(reaction_in_model)
found, rxn = cerm.check_for_existing_reaction(reaction_to_add)
self.assertTrue(
found,
'check_for_existing_reaction failed to eliminate reactions without duplicate tag'
)
def test_check_for_existing_reaction_eliminates_identical_reactions(self):
"""
Test that check_for_existing_reaction catches identical reactions.
"""
cerm = CoreEdgeReactionModel()
# make species' objects
spcA = Species().from_smiles('[H]')
spcB = Species().from_smiles('C=C[CH2]C')
spcC = Species().from_smiles('C=C=CC')
spcD = Species().from_smiles('[H][H]')
spcA.label = '[H]'
spcB.label = 'C=C[CH2]C'
spcC.label = 'C=C=CC'
spcD.label = '[H][H]'
spcB.generate_resonance_structures()
cerm.add_species_to_core(spcA)
cerm.add_species_to_core(spcB)
cerm.add_species_to_core(spcC)
cerm.add_species_to_core(spcD)
reaction_in_model = TemplateReaction(reactants=[spcA, spcB],
products=[spcC, spcD],
family='H_Abstraction',
template=['Csd', 'H'])
reaction_in_model.reactants.sort()
reaction_in_model.products.sort()
reaction_to_add = TemplateReaction(reactants=[spcA, spcB],
products=[spcC, spcD],
family='H_Abstraction',
template=['Csd', 'H'])
cerm.add_reaction_to_core(reaction_in_model)
cerm.register_reaction(reaction_in_model)
found, rxn = cerm.check_for_existing_reaction(reaction_to_add)
self.assertTrue(
found,
'check_for_existing_reaction failed to identify existing reaction')