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Tests: Modifications to reaction tests
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@alongd
alongd committed Jun 28, 2024
1 parent d1ee682 commit b09a96f
Showing 1 changed file with 10 additions and 63 deletions.
73 changes: 10 additions & 63 deletions arc/reaction_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,23 +167,16 @@ def test_as_dict(self):
self.rxn1.determine_family(self.rmgdb)
rxn_dict_1 = self.rxn1.as_dict()
# mol.atoms are not tested since all id's (including connectivity) changes depending on how the test is run.
expected_dict_1 = {'charge': 0,
'family': 'H_Abstraction',
expected_dict_1 = {'family': 'H_Abstraction',
'family_own_reverse': True,
'index': None,
'label': 'CH4 + OH <=> CH3 + H2O',
'multiplicity': 2,
'p_species': [{'arkane_file': None,
'bond_corrections': {'C-H': 3},
'charge': 0,
'p_species': [{'bond_corrections': {'C-H': 3},
'cheap_conformer': 'C 0.00000000 0.00000001 -0.00000000\n'
'H 1.06690511 -0.17519582 0.05416493\n'
'H -0.68531716 -0.83753536 -0.02808565\n'
'H -0.38158795 1.01273118 -0.02607927',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'CH3',
'long_thermo_description': "Bond corrections: {'C-H': 3}\n",
'mol': {'atom_order': rxn_dict_1['p_species'][0]['mol']['atom_order'],
Expand All @@ -192,16 +185,10 @@ def test_as_dict(self):
'props': {}},
'multiplicity': 2,
'number_of_rotors': 0},
{'arkane_file': None,
'bond_corrections': {'H-O': 2},
'charge': 0,
{'bond_corrections': {'H-O': 2},
'cheap_conformer': 'O -0.00032832 0.39781490 0.00000000\n'
'H -0.76330345 -0.19953755 0.00000000\n'
'H 0.76363177 -0.19827735 0.00000000',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'H2O',
'long_thermo_description': "Bond corrections: {'H-O': 2}\n",
'mol': {'atom_order': rxn_dict_1['p_species'][1]['mol']['atom_order'],
Expand All @@ -211,18 +198,12 @@ def test_as_dict(self):
'multiplicity': 1,
'number_of_rotors': 0}],
'products': ['CH3', 'H2O'],
'r_species': [{'arkane_file': None,
'bond_corrections': {'C-H': 4},
'charge': 0,
'r_species': [{'bond_corrections': {'C-H': 4},
'cheap_conformer': 'C -0.00000000 -0.00000000 0.00000000\n'
'H -0.63306457 -0.78034118 -0.42801448\n'
'H -0.38919244 0.98049560 -0.28294367\n'
'H 0.00329661 -0.09013273 1.08846898\n'
'H 1.01896040 -0.11002169 -0.37751083',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'CH4',
'long_thermo_description': "Bond corrections: {'C-H': 4}\n",
'mol': {'atom_order': rxn_dict_1['r_species'][0]['mol']['atom_order'],
Expand All @@ -231,15 +212,9 @@ def test_as_dict(self):
'props': {}},
'multiplicity': 1,
'number_of_rotors': 0},
{'arkane_file': None,
'bond_corrections': {'H-O': 1},
'charge': 0,
{'bond_corrections': {'H-O': 1},
'cheap_conformer': 'O 0.00000000 0.00000000 0.61310000\n'
'H 0.00000000 0.00000000 -0.61310000',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'OH',
'long_thermo_description': "Bond corrections: {'H-O': 1}\n",
'mol': {'atom_order': rxn_dict_1['r_species'][1]['mol']['atom_order'],
Expand All @@ -249,27 +224,18 @@ def test_as_dict(self):
'multiplicity': 2,
'number_of_rotors': 0}],
'reactants': ['CH4', 'OH'],
'ts_label': None,
}
self.assertEqual(rxn_dict_1, expected_dict_1)

rxn_dict_6 = self.rxn6.as_dict()
# The ``long_thermo_description`` attribute isn't deterministic (order could change)
expected_dict_6 = {'charge': 0,
'index': None,
'label': 'NH2 + N2H3 <=> NH3 + H2NN[S]',
expected_dict_6 = {'label': 'NH2 + N2H3 <=> NH3 + H2NN[S]',
'multiplicity': 1,
'p_species': [{'arkane_file': None,
'bond_corrections': {'H-N': 3},
'charge': 0,
'p_species': [{'bond_corrections': {'H-N': 3},
'cheap_conformer': 'N 0.00064924 -0.00099698 0.29559292\n'
'H -0.41786606 0.84210396 -0.09477452\n'
'H -0.52039228 -0.78225292 -0.10002797\n'
'H 0.93760911 -0.05885406 -0.10079043',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'NH3',
'long_thermo_description': "Bond corrections: {'H-N': 3}\n",
'mol': {'atom_order': rxn_dict_6['p_species'][0]['mol']['atom_order'],
Expand All @@ -278,22 +244,16 @@ def test_as_dict(self):
'props': {}},
'multiplicity': 1,
'number_of_rotors': 0},
{'arkane_file': None,
'adjlist': """multiplicity 1
{'adjlist': """multiplicity 1
1 N u0 p0 c+1 {2,D} {3,S} {4,S}
2 N u0 p2 c-1 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""",
'bond_corrections': {'H-N': 2, 'N=N': 1},
'charge': 0,
'cheap_conformer': 'N -0.08201544 0.01567102 0.28740725\n'
'N 1.12656450 -0.21525765 -0.48621674\n'
'H -0.50742562 -0.72901556 0.83982059\n'
'H -0.53712345 0.92860218 0.29862267',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'H2NN[S]',
'long_thermo_description': rxn_dict_6['p_species'][1]['long_thermo_description'],
'mol': {'atom_order': rxn_dict_6['p_species'][1]['mol']['atom_order'],
Expand All @@ -304,16 +264,10 @@ def test_as_dict(self):
'number_of_rotors': 0,
'original_label': 'H2NN(S)'}],
'products': ['H2NN[S]', 'NH3'],
'r_species': [{'arkane_file': None,
'bond_corrections': {'H-N': 2},
'charge': 0,
'r_species': [{'bond_corrections': {'H-N': 2},
'cheap_conformer': 'N 0.00016375 0.40059499 0.00000000\n'
'H -0.83170922 -0.19995756 0.00000000\n'
'H 0.83154548 -0.20063742 0.00000000',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'NH2',
'long_thermo_description': "Bond corrections: {'H-N': 2}\n",
'mol': {'atom_order': rxn_dict_6['r_species'][0]['mol']['atom_order'],
Expand All @@ -322,18 +276,12 @@ def test_as_dict(self):
'props': {}},
'multiplicity': 2,
'number_of_rotors': 0},
{'arkane_file': None,
'bond_corrections': {'H-N': 3, 'N-N': 1},
'charge': 0,
{'bond_corrections': {'H-N': 3, 'N-N': 1},
'cheap_conformer': 'N -0.46751749 0.03795671 0.31180026\n'
'N 0.79325823 -0.46038094 -0.24114357\n'
'H -1.19307188 -0.63034971 0.05027053\n'
'H -0.69753009 0.90231202 -0.17907452\n'
'H 1.56486123 0.15046192 0.05814730',
'compute_thermo': True,
'consider_all_diastereomers': True,
'force_field': 'MMFF94s',
'is_ts': False,
'label': 'N2H3',
'long_thermo_description': rxn_dict_6['r_species'][1]['long_thermo_description'],
'mol': {'atom_order': rxn_dict_6['r_species'][1]['mol']['atom_order'],
Expand All @@ -343,7 +291,6 @@ def test_as_dict(self):
'multiplicity': 2,
'number_of_rotors': 0}],
'reactants': ['N2H3', 'NH2'],
'ts_label': None,
}
self.assertEqual(rxn_dict_6, expected_dict_6)

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