def testIntraHmigration(self):
"""An intra-H migration reaction"""
self.loadDatabase(only_families=['intra_H_migration'])
structure1 = Structure()
structure1.fromSMILES("[CH](CCCc1ccccc1)CCCCCC")
species1 = makeNewSpecies(structure1)
structure2 = Structure()
structure2.fromSMILES("C(CCCC[CH]c1ccccc1)CCCC")
species2 = makeNewSpecies(structure2)
# wipe the reaction list
reaction.reactionList=[]
rxns = reaction.kineticsDatabase.getReactions([species1])
#for rxn in rxns:
# print 'Reaction family:',rxn.family
# print 'Reaction:',rxn
# print 'Kinetics:',rxn.kinetics
# print 'bestKinetics:',rxn.bestKinetics
# print
all_products = []
for rxn in rxns:
self.assertEqual(rxn.family.label,'Intra H migration',"Was trying to test 'Intra H migration' but made a reaction from family %s"%rxn.family)
self.assertEqual(len(rxn.reactants),1,"Reaction %s wasn't unimolecular"%rxn)
all_products.extend(rxn.products)
self.assertTrue(species2 in all_products, "None of the reactions made %s"%(species2))
def testEthaneExtrusionFromEther(self):
"""A reaction that was giving trouble in a diesel simulation"""
self.loadDatabase(only_families=['1,3_Insertion_ROR'])
structure1 = Structure()
structure1.fromSMILES("c1c([CH]C(C=CCCCCCC)OOCc2c3ccccc3ccc2)cccc1")
species1 = makeNewSpecies(structure1)
structure2 = Structure()
structure2.fromSMILES("c1ccc(c2ccccc12)COO")
species2 = makeNewSpecies(structure2)
structure3 = Structure()
structure3.fromSMILES("c1cc(C=C[C]=CCCCCCC)ccc1")
species3 = makeNewSpecies(structure3)
# wipe the reaction list
reaction.reactionList=[]
#print "FORWARD"
rxns = reaction.kineticsDatabase.getReactions([species2,species3])
#for rxn in rxns:
# print 'Reaction family:',rxn.family
# print 'Reaction:',rxn
# print 'Kinetics:',rxn.kinetics
# print 'bestKinetics:',rxn.bestKinetics
# print
self.assertEqual(len(rxns),18, "Was expecting to make 18 reactions for %s + %s"%(species2,species3))
# wipe the reaction list
reaction.reactionList=[]
#print "REVERSE"
rxns = reaction.kineticsDatabase.getReactions([species1])
#for rxn in rxns:
# print 'Reaction family:',rxn.family
# print 'Reaction:',rxn
# print 'Kinetics:',rxn.kinetics
# print 'bestKinetics:',rxn.bestKinetics
# print
self.assertEqual(len(rxns),1, "Was expecting to make 1 reaction for %s"%(species1))
rxn = rxns[0]
self.assertEqual(len(rxn.reactants),2,"Reaction wasn't bimolecular")
self.assertTrue(species2 in rxn.reactants, "Didn't make %s"%species2)
self.assertTrue(species3 in rxn.reactants, "Didn't make %s"%species3)
def test12Cycloaddition(self):
"""Test 1+2_Cycloaddition reactions"""
self.loadDatabase(only_families=['1+2_Cycloaddition'])
for smile in ['O1OO1'
]:
structure1 = Structure(SMILES=smile)
species1, isNew = makeNewSpecies(structure1)
print 'Reacting species',species1
# wipe the reaction list
reaction.reactionDict = {}
rxns = reaction.kineticsDatabase.getReactions([species1])
for rxn in rxns:
print 'Reaction family:',rxn.family
print 'Reaction:',rxn
print 'Kinetics:',rxn.kinetics
print
all_products = []
for rxn in rxns:
#self.assertEqual(rxn.family.label,'Cyclic colligation',"Was trying to test 'Cyclic colligation' but made a reaction from family %s"%rxn.family)
#self.assertEqual(len(rxn.reactants),1,"Reaction %s wasn't unimolecular"%rxn)
#self.assertEqual(len(rxn.products),1,"Reaction %s wasn't unimolecular"%rxn)
all_products.extend(rxn.products)
print "All products for reacting %s:"%species1, [p.structure[0] for p in all_products]
structure2 = Structure()
structure2.fromAdjacencyList("O2\n1 O 0 {2,D}\n2 O 0 {1,D}\n")
species2 = makeNewSpecies(structure2)
structure3 = Structure()
structure3.fromAdjacencyList("O\n1 O 2\n")
species3 = makeNewSpecies(structure3)
reaction.reactionDict = {}
print "Now reacting %s with %s:"%(species2, species3)
for sp in (species2, species3):
print sp.toAdjacencyList()
rxns = reaction.kineticsDatabase.getReactions([species2,species3])
for rxn in rxns:
print 'Reaction family:',rxn.family
print 'Reaction:',rxn
print 'Kinetics:',rxn.kinetics
self.assertEqual(len(rxns),1, "Made %d 1+2_Cycloaddition reactions instead of 1"%(len(rxns)))
def testMakeNewReaction(self):
"""Create a new reaction and check you can identify the reverse"""
structure1 = Structure()
structure1.fromAdjacencyList("""
1 C 0 {2,D} {7,S} {8,S}
2 C 0 {1,D} {3,S} {9,S}
3 C 0 {2,S} {4,D} {10,S}
4 C 0 {3,D} {5,S} {11,S}
5 *1 C 0 {4,S} {6,S} {12,S} {13,S}
6 C 0 {5,S} {14,S} {15,S} {16,S}
7 H 0 {1,S}
8 H 0 {1,S}
9 H 0 {2,S}
10 H 0 {3,S}
11 H 0 {4,S}
12 *2 H 0 {5,S}
13 H 0 {5,S}
14 H 0 {6,S}
15 H 0 {6,S}
16 H 0 {6,S}
""")
structure2 = Structure()
structure2.fromAdjacencyList("""
1 *3 H 1
""")
structure3 = Structure()
structure3.fromAdjacencyList("""
1 C 0 {2,D} {7,S} {8,S}
2 C 0 {1,D} {3,S} {9,S}
3 C 0 {2,S} {4,D} {10,S}
4 C 0 {3,D} {5,S} {11,S}
5 *3 C 1 {4,S} {6,S} {12,S}
6 C 0 {5,S} {13,S} {14,S} {15,S}
7 H 0 {1,S}
8 H 0 {1,S}
9 H 0 {2,S}
10 H 0 {3,S}
11 H 0 {4,S}
12 H 0 {5,S}
13 H 0 {6,S}
14 H 0 {6,S}
15 H 0 {6,S}
""")
structure4 = Structure()
structure4.fromAdjacencyList("""
1 *1 H 0 {2,S}
2 *2 H 0 {1,S}
""")
C6H10 = makeNewSpecies(structure1)
H = makeNewSpecies(structure2)
C6H9 = makeNewSpecies(structure3)
H2 = makeNewSpecies(structure4)
# wipe the reaction list
reaction.reactionList=[]
reaction1, isNew = makeNewReaction([C6H9, H2], [C6H10, H], \
[C6H9.structure[0], H2.structure[0]], \
[C6H10.structure[0], H.structure[0]], \
None)
self.assertFalse(reaction1 is None)
self.assertTrue(isNew)
reaction2, isNew = makeNewReaction([C6H10, H], [C6H9, H2], \
[C6H10.structure[0], H.structure[0]], \
[C6H9.structure[0], H2.structure[0]], \
None)
self.assertTrue(reaction1 is reaction2)
self.assertFalse(isNew)
