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 test_generate_isotope_reactions_limited_labeling(self):
"""
shows that all isotope reactions are created with generateIsotopeReactions
with limits of two isotopes per molecule
"""
max_number_labels = 1
methyl = Species().from_smiles('[CH3]')
methyl_isotopologues = [methyl] + generate_isotopomers(
methyl, max_number_labels)
methane = Species().from_smiles('C')
methane_isotopologues = [methane] + generate_isotopomers(
methane, max_number_labels)
ethyl = Species().from_smiles('C[CH2]')
ethyl_isotopologues = [ethyl] + generate_isotopomers(
ethyl, max_number_labels)
ethane = Species().from_smiles('CC')
ethane_isotopologues = [ethane] + generate_isotopomers(
ethane, max_number_labels)
self.assertEqual(len(methyl_isotopologues), 2)
self.assertEqual(len(methane_isotopologues), 2)
self.assertEqual(len(ethane_isotopologues), 2)
self.assertEqual(len(ethyl_isotopologues), 3)
reaction = TemplateReaction(reactants=[ethyl, methane],
products=[ethane, methyl],
family='H_Abstraction',
template=['C/H4', 'Y_rad'],
degeneracy=4)
reaction.kinetics = Arrhenius(A=(1e5, 'cm^3/(mol*s)'), Ea=(0, 'J/mol'))
isotope_list = [
methyl_isotopologues, methane_isotopologues, ethyl_isotopologues,
ethane_isotopologues
]
new_reactions = generate_isotope_reactions([reaction], isotope_list)
self.assertEqual(len(new_reactions), 6)
degeneracies_found = set()
for rxn in new_reactions:
self.assertEqual(rxn.template, reaction.template)
degeneracies_found.add(rxn.degeneracy)
self.assertIsNotNone(
rxn.kinetics,
'kinetics not obtained for reaction {}.'.format(rxn))
self.assertAlmostEqual(
reaction.kinetics.get_rate_coefficient(298),
rxn.kinetics.get_rate_coefficient(298) * reaction.degeneracy /
rxn.degeneracy)
self.assertEqual(degeneracies_found, set([4]))
def testGenerateIsotopeReactionsLimitedLabeling(self):
"""
shows that all isotope reactions are created with generateIsotopeReactions
with limits of two isotopes per molecule
"""
max_number_labels = 1
methyl = Species().fromSMILES('[CH3]')
methyl_isotopologues = [methyl] + generate_isotopomers(methyl,max_number_labels)
methane = Species().fromSMILES('C')
methane_isotopologues = [methane] + generate_isotopomers(methane,max_number_labels)
ethyl = Species().fromSMILES('C[CH2]')
ethyl_isotopologues = [ethyl] + generate_isotopomers(ethyl,max_number_labels)
ethane = Species().fromSMILES('CC')
ethane_isotopologues = [ethane] + generate_isotopomers(ethane,max_number_labels)
self.assertEqual(len(methyl_isotopologues),2)
self.assertEqual(len(methane_isotopologues),2)
self.assertEqual(len(ethane_isotopologues),2)
self.assertEqual(len(ethyl_isotopologues),3)
reaction = TemplateReaction(reactants = [ethyl,methane],
products = [ethane,methyl],
family = 'H_Abstraction',
template = ['C/H4', 'Y_rad'],
degeneracy = 4)
reaction.kinetics = Arrhenius(A=(1e5,'cm^3/(mol*s)'),Ea=(0,'J/mol'))
isotope_list = [methyl_isotopologues,
methane_isotopologues,
ethyl_isotopologues,
ethane_isotopologues]
new_reactions = generate_isotope_reactions([reaction], isotope_list)
self.assertEqual(len(new_reactions), 6)
degeneracies_found = set()
for rxn in new_reactions:
self.assertEqual(rxn.template, reaction.template)
degeneracies_found.add(rxn.degeneracy)
self.assertIsNotNone(rxn.kinetics,'kinetics not obtained for reaction {}.'.format(rxn))
self.assertAlmostEqual(reaction.kinetics.getRateCoefficient(298),
rxn.kinetics.getRateCoefficient(298) *\
reaction.degeneracy / rxn.degeneracy)
self.assertEqual(degeneracies_found, set([4]))
def testGenerateIsotopeReactions(self):
"""
shows that all isotope reactions are created with generateIsotopeReactions
"""
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().fromAdjacencyList(
"""
1 C u0 p0 c0 {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}
""")
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}
""")
craigie = Species().fromAdjacencyList(
"""
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
craigiei = Species().fromAdjacencyList(
"""
multiplicity 3
1 C u2 p0 c0 i13 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
reaction = TemplateReaction(reactants = [methyl,methyl],
products = [methane,craigie],
family = 'H_Abstraction',
template = ['Xrad_H', 'Y_rad'],
degeneracy = 3)
reaction.kinetics = Arrhenius(A=(1e5,'cm^3/(mol*s)'),Ea=(0,'J/mol'))
isotope_list = [[methyl,methyli],
[methane,methanei],
[craigie,craigiei]]
new_reactions = generate_isotope_reactions([reaction], isotope_list)
self.assertEqual(len(new_reactions), 4)
degeneracies_found = set()
for rxn in new_reactions:
self.assertEqual(rxn.template, reaction.template)
degeneracies_found.add(rxn.degeneracy)
self.assertIsNotNone(rxn.kinetics,'kinetics not obtained for reaction {}.'.format(rxn))
self.assertAlmostEqual(reaction.kinetics.getRateCoefficient(298),
rxn.kinetics.getRateCoefficient(298) *\
reaction.degeneracy / rxn.degeneracy)
self.assertEqual(degeneracies_found, set([3]))
def test_generate_isotope_reactions(self):
"""
shows that all isotope reactions are created with generateIsotopeReactions
"""
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_adjacency_list("""
1 C u0 p0 c0 {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}
""")
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}
""")
craigie = Species().from_adjacency_list("""
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
craigiei = Species().from_adjacency_list("""
multiplicity 3
1 C u2 p0 c0 i13 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
reaction = TemplateReaction(reactants=[methyl, methyl],
products=[methane, craigie],
family='H_Abstraction',
template=['Xrad_H', 'Y_rad'],
degeneracy=3)
reaction.kinetics = Arrhenius(A=(1e5, 'cm^3/(mol*s)'), Ea=(0, 'J/mol'))
isotope_list = [[methyl, methyli],
[methane, methanei],
[craigie, craigiei]]
new_reactions = generate_isotope_reactions([reaction], isotope_list)
self.assertEqual(len(new_reactions), 4)
degeneracies_found = set()
for rxn in new_reactions:
self.assertEqual(rxn.template, reaction.template)
degeneracies_found.add(rxn.degeneracy)
self.assertIsNotNone(rxn.kinetics, 'kinetics not obtained for reaction {}.'.format(rxn))
self.assertAlmostEqual(reaction.kinetics.get_rate_coefficient(298),
rxn.kinetics.get_rate_coefficient(298) * reaction.degeneracy / rxn.degeneracy)
self.assertEqual(degeneracies_found, set([3]))
