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f! fam tests
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@alongd
alongd committed Jul 29, 2024
1 parent 6f7392e commit 12d0085
Showing 1 changed file with 85 additions and 9 deletions.
94 changes: 85 additions & 9 deletions arc/reaction/family_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
ARC_FAMILIES_PATH,
RMG_DB_PATH,
add_labels_to_molecule,
check_product_isomorphism,
descent_complex_group,
determine_possible_reaction_products_from_family,
get_reaction_family_products,
Expand Down Expand Up @@ -131,16 +132,40 @@ def test_get_reaction_family_products(self):
rxn_0b = ARCReaction(r_species=[ARCSpecies(label='CH4', xyz=ch4_xyz), ARCSpecies(label='O2', xyz=o2_xyz, multiplicity=3)],
p_species=[ARCSpecies(label='CH3', xyz=ch3_xyz), ARCSpecies(label='HO2', xyz=ho2_xyz)])
products = get_reaction_family_products(rxn_0b)
expected_products = [{'discovered_in_reverse': True,
'family': 'Disproportionation', # Todo: should be H_abs after merging Calvin's PR
'group_labels': 'Root',
'label_map': {'*1': 0, '*2': 4, '*3': 5, '*4': 6},
'own_reverse': False,
'products': [Molecule(smiles="C"), Molecule(smiles="O=O")]}]
print(products)
expected_products = [{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 1, '*3': 5},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 1, '*3': 6},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 2, '*3': 5},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 2, '*3': 6},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 3, '*3': 5},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 3, '*3': 6},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 4, '*3': 5},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="[O]O"), Molecule(smiles="[CH3]")],
'label_map': {'*1': 0, '*2': 4, '*3': 6},
'own_reverse': True, 'discovered_in_reverse': False}]
self.assertEqual(products, expected_products)


rxn_1 = ARCReaction(reactants=['NH2', 'NH2'], products=['NH', 'NH3'],
r_species=[ARCSpecies(label='NH2', smiles='[NH2]')],
p_species=[ARCSpecies(label='NH', smiles='[NH]'), ARCSpecies(label='NH3', smiles='N')])
Expand Down Expand Up @@ -354,7 +379,13 @@ def test_get_reaction_family_products(self):
'group_labels': ('R_R', 'OJ_sec'),
'label_map': {'*1': 1, '*2': 0, '*3': 6},
'own_reverse': False,
'products': [Molecule(smiles="[CH2]C(=O)OO")]}]
'products': [Molecule(smiles="[CH2]C(=O)OO")]},
{'discovered_in_reverse': True,
'family': 'R_Addition_MultipleBond',
'group_labels': ('R_R', 'OJ_sec'),
'label_map': {'*1': 1, '*2': 2, '*3': 6},
'own_reverse': False,
'products': [Molecule(smiles="C=C([O])OO")]}]
self.assertEqual(products, expected_products)

rxn_8 = ARCReaction(r_species=[ARCSpecies(label='C3H7O2a', smiles='C[CH]COO')],
Expand Down Expand Up @@ -409,6 +440,23 @@ def test_get_reaction_family_products(self):
'products': [Molecule(smiles="[CH2]CCCCC")]}]
self.assertEqual(products, expected_products)

def test_get_reaction_family_products_considering_resonance(self):
"""Test determining the reaction family using product dicts for the non-trivial resonance structure"""
rxn_0a = ARCReaction(r_species=[ARCSpecies(label='R1', smiles='CC(C=S)S'),
ARCSpecies(label='R2', smiles='C=C[CH]C')],
p_species=[ARCSpecies(label='P1', smiles='[S]C=C(S)C'),
ARCSpecies(label='P2', smiles='C=CCC')])
products = get_reaction_family_products(rxn_0a)
expected_products = [{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="C=CCC"), Molecule(smiles="C[C](C=S)S")],
'label_map': {'*1': 1, '*2': 8, '*3': 13},
'own_reverse': True, 'discovered_in_reverse': False},
{'family': 'H_Abstraction', 'group_labels': ('X_H', 'Y_rad'),
'products': [Molecule(smiles="C=CCC"), Molecule(smiles="C[C](C=S)S")],
'label_map': {'*1': 1, '*2': 8, '*3': 13},
'own_reverse': True, 'discovered_in_reverse': False}]
self.assertEqual(products, expected_products)

def test_determine_possible_reaction_products_from_family(self):
"""Test determining the possible reaction products from a family"""
rxn_1 = ARCReaction(r_species=[ARCSpecies(label='nC3H7', smiles='[CH2]CC')],
Expand Down Expand Up @@ -446,6 +494,34 @@ def test_determine_possible_reaction_products_from_family(self):
'products': [Molecule(smiles="C[CH]C")]}]
self.assertEqual(product_dicts, expected_product_dicts)

def test_check_product_isomorphism(self):
"""Test checking product isomorphism"""
product_1 = Molecule(smiles='C[CH]C')
product_2 = ARCSpecies(label='S1', mol=Molecule(smiles='C[CH]C'))
self.assertTrue(check_product_isomorphism([product_1], [product_2]))
product_2 = ARCSpecies(label='S1', mol=Molecule(smiles='[CH2]CC'))
self.assertFalse(check_product_isomorphism([product_1], [product_2]))

product_1 = Molecule(smiles='C=C[O]')
product_2 = ARCSpecies(label='S1', mol=Molecule(smiles='[CH2]C=O'))
self.assertTrue(check_product_isomorphism([product_1], [product_2]))

product_1 = Molecule(smiles='C[C](C=S)S')
product_2 = ARCSpecies(label='S1', mol=Molecule(smiles='[S]C=C(S)C'))
self.assertTrue(check_product_isomorphism([product_1], [product_2]))

product_1 = Molecule(smiles='[CH2]C(C=S)S')
self.assertFalse(check_product_isomorphism([product_1], [product_2]))

products = [Molecule(smiles="[CH2]C(C=S)S")]
p_species = [ARCSpecies(label="P1", smiles="[S]C=C(S)C", is_ts=False, multiplicity=2, charge=0),]
self.assertFalse(check_product_isomorphism(products, p_species))

products = [Molecule(smiles="C=CCC"), Molecule(smiles="[CH2]C(C=S)S")]
p_species = [ARCSpecies(label="P1", smiles="[S]C=C(S)C", is_ts=False, multiplicity=2, charge=0),
ARCSpecies(label="P2", smiles="C=CCC", is_ts=False, multiplicity=1, charge=0)]
self.assertFalse(check_product_isomorphism(products, p_species))

def test_get_all_families(self):
"""Test getting all families from RMG and/or ARC"""
families = get_all_families(consider_arc_families=False)
Expand Down

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