def test_ensure_reaction_direction_with_multiple_ts(self):
"""Tests that ensure reaction direction can handle multiple transition states"""
family = self.database.kinetics.families['intra_H_migration']
r = Molecule().from_smiles("[CH2]CCC")
p = Molecule().from_smiles("C[CH]CC")
rxn = TemplateReaction(reactants=[r], products=[p])
family.add_atom_labels_for_reaction(reaction=rxn)
rxn.template = family.get_reaction_template_labels(reaction=rxn)
rxn.degeneracy = family.calculate_degeneracy(rxn)
rxn.family = 'intra_H_migration'
rxn.kinetics = Arrhenius(A=(1, 's^-1'))
ri = Molecule().from_adjacency_list("""
multiplicity 2
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 i13 {1,S} {5,S} {7,S} {8,S}
5 C u0 p0 c0 i13 {4,S} {6,S} {9,S} {10,S}
6 C u0 p0 c0 {5,S} {11,S} {12,S} {13,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {4,S}
9 H u0 p0 c0 {5,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {6,S}
12 H u0 p0 c0 {6,S}
13 H u0 p0 c0 {6,S}
""")
pi = Molecule().from_adjacency_list("""
multiplicity 2
1 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S}
2 C u1 p0 c0 i13 {1,S} {3,S} {4,S}
3 H u0 p0 c0 {2,S}
4 C u0 p0 c0 i13 {2,S} {5,S} {9,S} {10,S}
5 C u0 p0 c0 {4,S} {11,S} {12,S} {13,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {4,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {5,S}
""")
rxni = TemplateReaction(reactants=[pi],
products=[ri],
pairs=[[pi, ri]])
family.add_atom_labels_for_reaction(reaction=rxni)
rxni.template = family.get_reaction_template_labels(reaction=rxni)
rxn_cluster = [rxn, rxni]
ensure_reaction_direction(rxn_cluster)
self.assertEqual(rxn_cluster[0].degeneracy, 2)
self.assertEqual(rxn_cluster[1].degeneracy, 2)
self.assertIn('R2Hall', rxn_cluster[0].template)
self.assertIn('R2Hall', rxn_cluster[1].template)
self.assertAlmostEqual(
rxn_cluster[0].kinetics.get_rate_coefficient(298),
rxn_cluster[1].kinetics.get_rate_coefficient(298))
def test_ensure_reaction_direction_with_multiple_TS(self):
"""Tests that ensure reaction direction can handle multiple transition states"""
family = self.database.kinetics.families['intra_H_migration']
r = Molecule().fromSMILES("[CH2]CCC")
p = Molecule().fromSMILES("C[CH]CC")
rxn = TemplateReaction(reactants=[r], products=[p])
family.addAtomLabelsForReaction(reaction=rxn)
rxn.template = family.getReactionTemplateLabels(reaction=rxn)
rxn.degeneracy = family.calculateDegeneracy(rxn)
rxn.family = 'intra_H_migration'
rxn.kinetics = Arrhenius(A=(1,'s^-1'))
ri = Molecule().fromAdjacencyList("""
multiplicity 2
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 i13 {1,S} {5,S} {7,S} {8,S}
5 C u0 p0 c0 i13 {4,S} {6,S} {9,S} {10,S}
6 C u0 p0 c0 {5,S} {11,S} {12,S} {13,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {4,S}
9 H u0 p0 c0 {5,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {6,S}
12 H u0 p0 c0 {6,S}
13 H u0 p0 c0 {6,S}
""")
pi = Molecule().fromAdjacencyList("""
multiplicity 2
1 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S}
2 C u1 p0 c0 i13 {1,S} {3,S} {4,S}
3 H u0 p0 c0 {2,S}
4 C u0 p0 c0 i13 {2,S} {5,S} {9,S} {10,S}
5 C u0 p0 c0 {4,S} {11,S} {12,S} {13,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {4,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {5,S}
""")
rxni = TemplateReaction(reactants=[pi], products=[ri],pairs=[[pi,ri]])
family.addAtomLabelsForReaction(reaction=rxni)
rxni.template = family.getReactionTemplateLabels(reaction=rxni)
rxn_cluster = [rxn,rxni]
ensure_reaction_direction(rxn_cluster)
self.assertEqual(rxn_cluster[0].degeneracy, 2)
self.assertEqual(rxn_cluster[1].degeneracy, 2)
self.assertIn('R2Hall', rxn_cluster[0].template)
self.assertIn('R2Hall', rxn_cluster[1].template)
self.assertAlmostEqual(rxn_cluster[0].kinetics.getRateCoefficient(298),
rxn_cluster[1].kinetics.getRateCoefficient(298))
def testEnsureReactionDirection(self):
"""
Tests that the direction of the reaction is constant for every isotopomer
"""
# get reactions
methyl = Species().fromSMILES('[CH3]')
methyli = Species().fromAdjacencyList(
"""
multiplicity 2
1 C u1 p0 c0 i13 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
methane = Species().fromSMILES('C')
methanei = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 i13 {2,S} {3,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
""")
dipropyl = Species().fromSMILES('[CH2]C[CH2]')
dipropyli = Species().fromAdjacencyList("""
multiplicity 3
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {8,S} {9,S}
5 C u1 p0 c0 i13 {4,S} {6,S} {7,S}
6 H u0 p0 c0 {5,S}
7 H u0 p0 c0 {5,S}
8 H u0 p0 c0 {4,S}
9 H u0 p0 c0 {4,S}
""")
propyl = Species().fromSMILES('CC[CH2]')
propyli = Species().fromAdjacencyList("""
multiplicity 2
1 C u1 p0 c0 i13 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {6,S} {7,S}
5 C u0 p0 c0 {4,S} {8,S} {9,S} {10,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {5,S}
9 H u0 p0 c0 {5,S}
10 H u0 p0 c0 {5,S}
""")
propyl.label='propyl'
propyli.label='propyli'
dipropyl.label = 'dipropyl'
dipropyli.label = 'dipropyli'
methyl.label = 'methyl'
methyli.label = 'methyli'
methane.label = 'methane'
methanei.label = 'methanei'
# make reactions
rxn1 = TemplateReaction(reactants=[dipropyl, methane],
products =[methyl, propyl],
kinetics = Arrhenius(A=(1.,'cm^3/(mol*s)'), Ea = (2., 'kJ/mol'), n=0.),
family = 'H_Abstraction',
template = ['a','c'],
degeneracy = 8,
pairs = [[methane,methyl],[dipropyl,propyl]])
rxn2 = TemplateReaction(reactants=[methyli, propyl],
products =[methanei, dipropyl],
kinetics = Arrhenius(A=(1e-20,'cm^3/(mol*s)'), Ea = (2., 'kJ/mol'), n=0.),
family = 'H_Abstraction',
template = ['b','d'],
degeneracy = 3,
pairs = [[methyli,methanei],[propyl,dipropyl]])
rxn3 = TemplateReaction(reactants=[methane, dipropyli],
products =[methyl, propyli],
kinetics = Arrhenius(A=(0.5,'cm^3/(mol*s)'), Ea = (2., 'kJ/mol'), n=0.),
family = 'H_Abstraction',
template = ['a','c'],
degeneracy = 4,
pairs = [[methane,methyl],[dipropyli,propyli]])
rxn4 = TemplateReaction(reactants=[methyli, propyli],
products =[methanei, dipropyli],
kinetics = Arrhenius(A=(1e-20,'cm^3/(mol*s)'), Ea = (2., 'kJ/mol'), n=0.),
family = 'H_Abstraction',
template = ['d','b'],
degeneracy = 3,
pairs = [[methyli,methanei],[propyli,dipropyli]])
rxns = [rxn1, rxn2, rxn3, rxn4]
# call method
ensure_reaction_direction(rxns)
for rxn in rxns:
# ensure there is a methane in reactants for each reaction
self.assertTrue(any([compare_isotopomers(methane, reactant) for reactant in rxn.reactants]),msg='ensureReactionDirection didnt flip the proper reactants and products')
# ensure kinetics is correct
if any([dipropyli.isIsomorphic(reactant) for reactant in rxn.reactants]):
self.assertAlmostEqual(rxn.kinetics.A.value, 0.5, msg= 'The A value returned, {0}, is incorrect. Check the reactions degeneracy and how A.value is obtained. The reaction is:{1}'.format(rxn.kinetics.A.value, rxn))
else:
self.assertAlmostEqual(rxn.kinetics.A.value, 1. , msg='The A value returned, {0}, is incorrect. Check the reactions degeneracy and how A.value is obtained. The reaction is:{1}'.format(rxn.kinetics.A.value, rxn))
def test_ensure_reaction_direction(self):
"""
Tests that the direction of the reaction is constant for every isotopomer
"""
# get reactions
methyl = Species().from_smiles('[CH3]')
methyli = Species().from_adjacency_list("""
multiplicity 2
1 C u1 p0 c0 i13 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
methane = Species().from_smiles('C')
methanei = Species().from_adjacency_list("""
1 C u0 p0 c0 i13 {2,S} {3,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
""")
dipropyl = Species().from_smiles('[CH2]C[CH2]')
dipropyli = Species().from_adjacency_list("""
multiplicity 3
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {8,S} {9,S}
5 C u1 p0 c0 i13 {4,S} {6,S} {7,S}
6 H u0 p0 c0 {5,S}
7 H u0 p0 c0 {5,S}
8 H u0 p0 c0 {4,S}
9 H u0 p0 c0 {4,S}
""")
propyl = Species().from_smiles('CC[CH2]')
propyli = Species().from_adjacency_list("""
multiplicity 2
1 C u1 p0 c0 i13 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {6,S} {7,S}
5 C u0 p0 c0 {4,S} {8,S} {9,S} {10,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {5,S}
9 H u0 p0 c0 {5,S}
10 H u0 p0 c0 {5,S}
""")
propyl.label = 'propyl'
propyli.label = 'propyli'
dipropyl.label = 'dipropyl'
dipropyli.label = 'dipropyli'
methyl.label = 'methyl'
methyli.label = 'methyli'
methane.label = 'methane'
methanei.label = 'methanei'
# make reactions
rxn1 = TemplateReaction(reactants=[dipropyl, methane],
products=[methyl, propyl],
kinetics=Arrhenius(A=(1., 'cm^3/(mol*s)'), Ea=(2., 'kJ/mol'), n=0.),
family='H_Abstraction',
template=['a', 'c'],
degeneracy=8,
pairs=[[methane, methyl], [dipropyl, propyl]])
rxn2 = TemplateReaction(reactants=[methyli, propyl],
products=[methanei, dipropyl],
kinetics=Arrhenius(A=(1e-20, 'cm^3/(mol*s)'), Ea=(2., 'kJ/mol'), n=0.),
family='H_Abstraction',
template=['b', 'd'],
degeneracy=3,
pairs=[[methyli, methanei], [propyl, dipropyl]])
rxn3 = TemplateReaction(reactants=[methane, dipropyli],
products=[methyl, propyli],
kinetics=Arrhenius(A=(0.5, 'cm^3/(mol*s)'), Ea=(2., 'kJ/mol'), n=0.),
family='H_Abstraction',
template=['a', 'c'],
degeneracy=4,
pairs=[[methane, methyl], [dipropyli, propyli]])
rxn4 = TemplateReaction(reactants=[methyli, propyli],
products=[methanei, dipropyli],
kinetics=Arrhenius(A=(1e-20, 'cm^3/(mol*s)'), Ea=(2., 'kJ/mol'), n=0.),
family='H_Abstraction',
template=['d', 'b'],
degeneracy=3,
pairs=[[methyli, methanei], [propyli, dipropyli]])
rxns = [rxn1, rxn2, rxn3, rxn4]
# call method
ensure_reaction_direction(rxns)
for rxn in rxns:
# ensure there is a methane in reactants for each reaction
self.assertTrue(any([compare_isotopomers(methane, reactant) for reactant in rxn.reactants]),
msg='ensureReactionDirection didnt flip the proper reactants and products')
# ensure kinetics is correct
if any([dipropyli.is_isomorphic(reactant) for reactant in rxn.reactants]):
self.assertAlmostEqual(rxn.kinetics.A.value, 0.5,
msg='The A value returned, {0}, is incorrect. '
'Check the reactions degeneracy and how A.value is obtained. '
'The reaction is:{1}'.format(rxn.kinetics.A.value, rxn))
else:
self.assertAlmostEqual(rxn.kinetics.A.value, 1.,
msg='The A value returned, {0}, is incorrect. '
'Check the reactions degeneracy and how A.value is obtained. '
'The reaction is:{1}'.format(rxn.kinetics.A.value, rxn))