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alongd merged 2 commits into from
Apr 28, 2026
Merged

Break down monolithic driver and heuristics tests #881

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fae214f
Break down heuristics tests
alongd Apr 25, 2026
0d22e94
Break down driver tests
alongd Apr 27, 2026
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240 changes: 105 additions & 135 deletions arc/job/adapters/ts/heuristics_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1125,63 +1125,58 @@ def test_heuristics_for_h_abstraction_13(self):
heuristics_1.execute_incore()
self.assertEqual(len(rxn1.ts_species.ts_guesses), 12)

def test_heuristics_for_hydrolysis(self):
def test_heuristics_for_carbonyl_based_hydrolysis(self):
"""
Test that ARC can generate TS guesses based on heuristics for different hydrolysis families reactions.
Test heuristics for carbonyl-based hydrolysis: C2H4O2 + H2O <=> CH2O2 + CH4O.
"""
# Carbonyl-based hydrolysis
# C2H4O2 + H2O <=> CH2O2 + CH4O
methylformate = self.methylformate
formicacid = self.formicacid
methanol = self.methanol
water = self.water
rxn1 = ARCReaction(r_species=[methylformate, water], p_species=[formicacid, methanol],
family='carbonyl_based_hydrolysis')
heuristics_1 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn1],
testing=True,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'heuristics')
)
heuristics_1.execute_incore()
self.assertEqual(rxn1.family, 'carbonyl_based_hydrolysis')
self.assertTrue(rxn1.ts_species.is_ts)
self.assertEqual(rxn1.ts_species.ts_guesses[0].initial_xyz['symbols'],
rxn = ARCReaction(r_species=[self.methylformate, self.water],
p_species=[self.formicacid, self.methanol],
family='carbonyl_based_hydrolysis')
adapter = HeuristicsAdapter(job_type='tsg',
reactions=[rxn],
testing=True,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'heuristics_carbonyl'))
adapter.execute_incore()
self.assertEqual(rxn.family, 'carbonyl_based_hydrolysis')
self.assertTrue(rxn.ts_species.is_ts)
self.assertEqual(rxn.ts_species.ts_guesses[0].initial_xyz['symbols'],
('C', 'O', 'C', 'O', 'H', 'H', 'H', 'H', 'O', 'H', 'H'))
self.assertEqual(len(rxn1.ts_species.ts_guesses), 6)
# Ether hydrolysis
# C3H8O + H2O <=> C2H6O + CH4O
allylmethylether = self.allylmethylether
allylalcohol = self.allylalcohol
methanol = self.methanol
rxn2 = ARCReaction(r_species=[allylmethylether, water], p_species=[allylalcohol, methanol])
heuristics_2 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn2],
testing=True,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'heuristics')
)
heuristics_2.execute_incore()
self.assertEqual(rxn2.family, 'ether_hydrolysis')
self.assertTrue(rxn2.ts_species.is_ts)
self.assertEqual(rxn2.ts_species.ts_guesses[0].initial_xyz['symbols'],
self.assertEqual(len(rxn.ts_species.ts_guesses), 6)

def test_heuristics_for_ether_hydrolysis(self):
"""
Test heuristics for ether hydrolysis: C3H8O + H2O <=> C2H6O + CH4O.
"""
rxn = ARCReaction(r_species=[self.allylmethylether, self.water],
p_species=[self.allylalcohol, self.methanol])
adapter = HeuristicsAdapter(job_type='tsg',
reactions=[rxn],
testing=True,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'heuristics_ether'))
adapter.execute_incore()
self.assertEqual(rxn.family, 'ether_hydrolysis')
self.assertTrue(rxn.ts_species.is_ts)
self.assertEqual(rxn.ts_species.ts_guesses[0].initial_xyz['symbols'],
('C', 'C', 'C', 'O', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'O', 'H', 'H'))
self.assertEqual(len(rxn2.ts_species.ts_guesses), 4)
# Nitrile hydrolysis
# N#CC(C#N) + H2O <=> N=C(O)C(C#N)
malononitrile = self.malononitrile
iminopropanoic_acid = self.iminopropanoic_acid
rxn4 = ARCReaction(r_species=[malononitrile, water], p_species=[iminopropanoic_acid])
heuristics_4 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn4],
testing=True,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'heuristics')
)
heuristics_4.execute_incore()
self.assertEqual(rxn4.family, 'nitrile_hydrolysis')
self.assertTrue(rxn4.ts_species.is_ts)
self.assertEqual(rxn4.ts_species.ts_guesses[0].initial_xyz['symbols'],
self.assertEqual(len(rxn.ts_species.ts_guesses), 4)

def test_heuristics_for_nitrile_hydrolysis(self):
"""
Test heuristics for nitrile hydrolysis: N#CC(C#N) + H2O <=> N=C(O)C(C#N).
"""
rxn = ARCReaction(r_species=[self.malononitrile, self.water],
p_species=[self.iminopropanoic_acid])
adapter = HeuristicsAdapter(job_type='tsg',
reactions=[rxn],
testing=True,
project='test',
project_directory=os.path.join(ARC_TESTING_PATH, 'heuristics_nitrile'))
adapter.execute_incore()
self.assertEqual(rxn.family, 'nitrile_hydrolysis')
self.assertTrue(rxn.ts_species.is_ts)
self.assertEqual(rxn.ts_species.ts_guesses[0].initial_xyz['symbols'],
('N', 'C', 'C', 'C', 'N', 'H', 'H', 'O', 'H', 'H'))

def test_keeping_atom_order_in_ts(self):
Expand Down Expand Up @@ -1958,90 +1953,65 @@ def test_find_distant_neighbor(self):
self.assertEqual(find_distant_neighbor(mol=mol_3, start=2), 4)
self.assertEqual(find_distant_neighbor(mol=mol_3, start=2), 4)

def test_are_h_abs_wells_reversed(self):
"""
Test the are_h_abs_wells_reversed() function.
The expected order is: R(*1)-H(*2) + R(*3)j <=> R(*1)j + R(*3)-H(*2)
"""
rxn_1 = ARCReaction(r_species=[ARCSpecies(label='C2H6', smiles='CC'), ARCSpecies(label='OH', smiles='[OH]')],
# none are reversed
p_species=[ARCSpecies(label='C2H5', smiles='[CH2]C'), ARCSpecies(label='H2O', smiles='O')])
rxn_2 = ARCReaction(r_species=[ARCSpecies(label='OH', smiles='[OH]'), ARCSpecies(label='C2H6', smiles='CC')],
# r reversed
p_species=[ARCSpecies(label='C2H5', smiles='[CH2]C'), ARCSpecies(label='H2O', smiles='O')])
rxn_3 = ARCReaction(r_species=[ARCSpecies(label='C2H6', smiles='CC'), ARCSpecies(label='OH', smiles='[OH]')],
# p reversed
p_species=[ARCSpecies(label='H2O', smiles='O'), ARCSpecies(label='C2H5', smiles='[CH2]C')])
rxn_4 = ARCReaction(r_species=[ARCSpecies(label='OH', smiles='[OH]'), ARCSpecies(label='C2H6', smiles='CC')],
# r and p reversed
p_species=[ARCSpecies(label='H2O', smiles='O'), ARCSpecies(label='C2H5', smiles='[CH2]C')])

product_dicts = get_reaction_family_products(rxn=rxn_1,
rmg_family_set=[rxn_1.family],
consider_rmg_families=True,
consider_arc_families=False,
discover_own_reverse_rxns_in_reverse=False,
)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn_1, product_dict=product_dicts[0])
self.assertFalse(r_reversed)
self.assertFalse(p_reversed)

product_dicts = get_reaction_family_products(rxn=rxn_2,
rmg_family_set=[rxn_2.family],
consider_rmg_families=True,
consider_arc_families=False,
discover_own_reverse_rxns_in_reverse=False,
)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn_2, product_dict=product_dicts[0])
self.assertTrue(r_reversed)
self.assertFalse(p_reversed)

product_dicts = get_reaction_family_products(rxn=rxn_3,
rmg_family_set=[rxn_3.family],
consider_rmg_families=True,
consider_arc_families=False,
discover_own_reverse_rxns_in_reverse=False,
)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn_3, product_dict=product_dicts[0])
self.assertFalse(r_reversed)
self.assertTrue(p_reversed)

product_dicts = get_reaction_family_products(rxn=rxn_4,
rmg_family_set=[rxn_4.family],
consider_rmg_families=True,
consider_arc_families=False,
discover_own_reverse_rxns_in_reverse=False,
)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn_4, product_dict=product_dicts[0])
self.assertTrue(r_reversed)
self.assertTrue(p_reversed)

rxn_5 = ARCReaction(r_species=[ARCSpecies(label='H', smiles='[H]'), ARCSpecies(label='H2O', smiles='O')],
# r and p reversed
p_species=[ARCSpecies(label='H2', smiles='[H][H]'), ARCSpecies(label='OH', smiles='[OH]')])
product_dicts = get_reaction_family_products(rxn=rxn_5,
rmg_family_set=[rxn_5.family],
consider_rmg_families=True,
consider_arc_families=False,
discover_own_reverse_rxns_in_reverse=False,
)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn_5, product_dict=product_dicts[0])
self.assertTrue(r_reversed)
self.assertTrue(p_reversed)

rxn_6 = ARCReaction(
r_species=[ARCSpecies(label='CCCC(O)=O', smiles='CCCC(O)=O'), ARCSpecies(label='OH', smiles='[OH]')],
# none are reversed
p_species=[ARCSpecies(label='CCCC([O])=O', smiles='CCCC([O])=O'), ARCSpecies(label='H2O', smiles='O')])
product_dicts = get_reaction_family_products(rxn=rxn_6,
rmg_family_set=[rxn_6.family],
def _check_h_abs_wells_reversed(self, rxn: 'ARCReaction', expected_r_reversed: bool, expected_p_reversed: bool):
"""Helper: run are_h_abs_wells_reversed against the family products and assert the orientations."""
product_dicts = get_reaction_family_products(rxn=rxn,
rmg_family_set=[rxn.family],
consider_rmg_families=True,
consider_arc_families=False,
discover_own_reverse_rxns_in_reverse=False,
)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn_6, product_dict=product_dicts[0])
self.assertFalse(r_reversed)
self.assertFalse(p_reversed)
r_reversed, p_reversed = are_h_abs_wells_reversed(rxn, product_dict=product_dicts[0])
self.assertEqual(r_reversed, expected_r_reversed)
self.assertEqual(p_reversed, expected_p_reversed)

def test_are_h_abs_wells_reversed_neither_reversed(self):
"""C2H6 + OH <=> C2H5 + H2O — neither r nor p reversed."""
rxn = ARCReaction(r_species=[ARCSpecies(label='C2H6', smiles='CC'),
ARCSpecies(label='OH', smiles='[OH]')],
p_species=[ARCSpecies(label='C2H5', smiles='[CH2]C'),
ARCSpecies(label='H2O', smiles='O')])
self._check_h_abs_wells_reversed(rxn, expected_r_reversed=False, expected_p_reversed=False)

def test_are_h_abs_wells_reversed_r_reversed(self):
"""OH + C2H6 <=> C2H5 + H2O — reactants reversed."""
rxn = ARCReaction(r_species=[ARCSpecies(label='OH', smiles='[OH]'),
ARCSpecies(label='C2H6', smiles='CC')],
p_species=[ARCSpecies(label='C2H5', smiles='[CH2]C'),
ARCSpecies(label='H2O', smiles='O')])
self._check_h_abs_wells_reversed(rxn, expected_r_reversed=True, expected_p_reversed=False)

def test_are_h_abs_wells_reversed_p_reversed(self):
"""C2H6 + OH <=> H2O + C2H5 — products reversed."""
rxn = ARCReaction(r_species=[ARCSpecies(label='C2H6', smiles='CC'),
ARCSpecies(label='OH', smiles='[OH]')],
p_species=[ARCSpecies(label='H2O', smiles='O'),
ARCSpecies(label='C2H5', smiles='[CH2]C')])
self._check_h_abs_wells_reversed(rxn, expected_r_reversed=False, expected_p_reversed=True)

def test_are_h_abs_wells_reversed_both_reversed(self):
"""OH + C2H6 <=> H2O + C2H5 — reactants and products reversed."""
rxn = ARCReaction(r_species=[ARCSpecies(label='OH', smiles='[OH]'),
ARCSpecies(label='C2H6', smiles='CC')],
p_species=[ARCSpecies(label='H2O', smiles='O'),
ARCSpecies(label='C2H5', smiles='[CH2]C')])
self._check_h_abs_wells_reversed(rxn, expected_r_reversed=True, expected_p_reversed=True)

def test_are_h_abs_wells_reversed_h_plus_h2o(self):
"""H + H2O <=> H2 + OH — reactants and products reversed."""
rxn = ARCReaction(r_species=[ARCSpecies(label='H', smiles='[H]'),
ARCSpecies(label='H2O', smiles='O')],
p_species=[ARCSpecies(label='H2', smiles='[H][H]'),
ARCSpecies(label='OH', smiles='[OH]')])
self._check_h_abs_wells_reversed(rxn, expected_r_reversed=True, expected_p_reversed=True)

def test_are_h_abs_wells_reversed_butyrate(self):
"""CCCC(O)=O + OH <=> CCCC([O])=O + H2O — neither r nor p reversed."""
rxn = ARCReaction(r_species=[ARCSpecies(label='CCCC(O)=O', smiles='CCCC(O)=O'),
ARCSpecies(label='OH', smiles='[OH]')],
p_species=[ARCSpecies(label='CCCC([O])=O', smiles='CCCC([O])=O'),
ARCSpecies(label='H2O', smiles='O')])
self._check_h_abs_wells_reversed(rxn, expected_r_reversed=False, expected_p_reversed=False)

def test_process_hydrolysis_reaction(self):
"""Test the process_hydrolysis_reaction() function."""
Expand Down Expand Up @@ -2254,8 +2224,8 @@ def tearDownClass(cls):
A function that is run ONCE after all unit tests in this class.
Delete all project directories created during these unit tests.
"""
shutil.rmtree(os.path.join(ARC_TESTING_PATH, 'heuristics'), ignore_errors=True)
shutil.rmtree(os.path.join(ARC_TESTING_PATH, 'heuristics_1'), ignore_errors=True)
for sub in ('heuristics', 'heuristics_1', 'heuristics_carbonyl', 'heuristics_ether', 'heuristics_nitrile'):
shutil.rmtree(os.path.join(ARC_TESTING_PATH, sub), ignore_errors=True)


if __name__ == '__main__':
Expand Down
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