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_calculate_degeneracy_for_non_reactive_molecule(self):
"""
tests that the calculateDegeneracy method gets the degeneracy correct for unreactive molecules
and that __generateReactions work correctly with the react_non_reactive flag set to `True`.
"""
from rmgpy.data.rmg import getDB
from rmgpy.data.kinetics.family import TemplateReaction
adjlist = [
'''
multiplicity 2
1 H u1 p0 c0''', '''
multiplicity 2
1 O u1 p1 c+1 {2,D}
2 N u0 p2 c-1 {1,D}''', '''
1 O u0 p1 c+1 {2,D} {3,S}
2 N u0 p2 c-1 {1,D}
3 H u0 p0 c0 {1,S}'''
]
family = getDB('kinetics').families['R_Recombination']
r1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[0])])
r2 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[1])
]) # r2 is not the representative structure of
# NO, but it is the correct structure participating in this reaction
p1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[2])])
r2.generate_resonance_structures(keep_isomorphic=True)
rxn = TemplateReaction(reactants=[r1, r2], products=[p1])
rxn.degeneracy = family.calculateDegeneracy(rxn)
self.assertEqual(rxn.degeneracy, 1)
def test_calculate_degeneracy_for_non_reactive_molecule(self):
"""
tests that the calculateDegeneracy method gets the degeneracy correct for unreactive molecules
and that __generateReactions work correctly with the react_non_reactive flag set to `True`.
"""
from rmgpy.data.rmg import getDB
from rmgpy.data.kinetics.family import TemplateReaction
adjlist = ['''
multiplicity 2
1 H u1 p0 c0''',
'''
multiplicity 2
1 O u1 p1 c+1 {2,D}
2 N u0 p2 c-1 {1,D}''',
'''
1 O u0 p1 c+1 {2,D} {3,S}
2 N u0 p2 c-1 {1,D}
3 H u0 p0 c0 {1,S}''']
family = getDB('kinetics').families['R_Recombination']
r1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[0])])
r2 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[1])]) # r2 is not the representative structure of
# NO, but it is the correct structure participating in this reaction
p1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[2])])
r2.generate_resonance_structures(keep_isomorphic=True)
rxn = TemplateReaction(reactants=[r1, r2], products=[p1])
rxn.degeneracy = family.calculateDegeneracy(rxn)
self.assertEqual(rxn.degeneracy, 1)
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 testaddReverseAttribute(self):
"""
tests that the addReverseAttribute method gets the reverse degeneracy correct
"""
from rmgpy.data.rmg import getDB
from rmgpy.data.kinetics.family import TemplateReaction
adjlist = [
'''
multiplicity 2
1 H u0 p0 c0 {7,S}
2 H u0 p0 c0 {4,S}
3 C u1 p0 c0 {5,S} {7,S} {8,S}
4 C u0 p0 c0 {2,S} {6,S} {7,D}
5 H u0 p0 c0 {3,S}
6 H u0 p0 c0 {4,S}
7 C u0 p0 c0 {1,S} {3,S} {4,D}
8 H u0 p0 c0 {3,S}
''', '''
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 i13 {1,S} {3,D} {7,S}
3 C u0 p0 c0 {2,D} {8,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {3,S}
''', '''
multiplicity 2
1 H u0 p0 c0 {7,S}
2 H u0 p0 c0 {4,S}
3 C u1 p0 c0 {5,S} {7,S} {8,S}
4 C u0 p0 c0 {2,S} {6,S} {7,D}
5 H u0 p0 c0 {3,S}
6 H u0 p0 c0 {4,S}
7 C u0 p0 c0 i13 {1,S} {3,S} {4,D}
8 H u0 p0 c0 {3,S}
''', '''
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,D} {7,S}
3 C u0 p0 c0 {2,D} {8,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {3,S}
'''
]
family = getDB('kinetics').families['H_Abstraction']
r1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[0])])
r2 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[1])])
p1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[2])])
p2 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[3])])
r1.generateResonanceIsomers(keepIsomorphic=True)
p1.generateResonanceIsomers(keepIsomorphic=True)
rxn = TemplateReaction(reactants=[r1, r2], products=[p1, p2])
rxn.degeneracy = family.calculateDegeneracy(rxn)
self.assertEqual(rxn.degeneracy, 6)
family.addReverseAttribute(rxn)
self.assertEqual(rxn.reverse.degeneracy, 6)
def testaddReverseAttribute(self):
"""
tests that the addReverseAttribute method gets the reverse degeneracy correct
"""
from rmgpy.data.rmg import getDB
from rmgpy.data.kinetics.family import TemplateReaction
adjlist = ['''
multiplicity 2
1 H u0 p0 c0 {7,S}
2 H u0 p0 c0 {4,S}
3 C u1 p0 c0 {5,S} {7,S} {8,S}
4 C u0 p0 c0 {2,S} {6,S} {7,D}
5 H u0 p0 c0 {3,S}
6 H u0 p0 c0 {4,S}
7 C u0 p0 c0 {1,S} {3,S} {4,D}
8 H u0 p0 c0 {3,S}
''',
'''
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 i13 {1,S} {3,D} {7,S}
3 C u0 p0 c0 {2,D} {8,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {3,S}
''',
'''
multiplicity 2
1 H u0 p0 c0 {7,S}
2 H u0 p0 c0 {4,S}
3 C u1 p0 c0 {5,S} {7,S} {8,S}
4 C u0 p0 c0 {2,S} {6,S} {7,D}
5 H u0 p0 c0 {3,S}
6 H u0 p0 c0 {4,S}
7 C u0 p0 c0 i13 {1,S} {3,S} {4,D}
8 H u0 p0 c0 {3,S}
''',
'''
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,D} {7,S}
3 C u0 p0 c0 {2,D} {8,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {3,S}
'''
]
family = getDB('kinetics').families['H_Abstraction']
r1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[0])])
r2 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[1])])
p1 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[2])])
p2 = Species(molecule=[Molecule().fromAdjacencyList(adjlist[3])])
r1.generate_resonance_structures(keep_isomorphic=True)
p1.generate_resonance_structures(keep_isomorphic=True)
rxn = TemplateReaction(reactants=[r1, r2], products=[p1, p2])
rxn.degeneracy = family.calculateDegeneracy(rxn)
self.assertEqual(rxn.degeneracy, 6)
family.addReverseAttribute(rxn)
self.assertEqual(rxn.reverse.degeneracy, 6)
