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 testSpeciesRestart(self):
"""
Restart tests for the :class:`rmg.species.Species` class.
"""
import rmg.structure as structure
import rmg.species as species
# Create
smiles = 'C=CC=C[CH]C'
struct0 = structure.Structure(SMILES=smiles)
spec0, isNew = species.makeNewSpecies(struct0, label=smiles, reactive=True)
# Pickle
f = open('test.pkl', 'wb'); cPickle.dump(spec0, f); f.close()
# Unpickle
f = open('test.pkl', 'rb'); spec = cPickle.load(f); f.close()
# Compare
self.assertTrue(spec0.id == spec.id)
self.assertTrue(spec0.label == spec.label == smiles)
self.assertTrue(spec0.reactive == spec.reactive == True)
self.assertTrue(len(spec0.structure) == len(spec.structure) == 3)
for struct1 in spec0.structure:
match = False
for struct2 in spec.structure:
if struct1.isIsomorphic(struct2): match = True
self.assertTrue(match)
self.assertTrue(spec0.thermoData.equals(spec.thermoData))
#self.assertTrue(spec0.thermoSnapshot == spec.thermoSnapshot)
self.assertTrue(spec0.spectralData == spec.spectralData)
self.assertTrue(spec0.lennardJones == spec.lennardJones)
def testCyclicColligation(self): """A test of a Birad_recombination (Cyclic colligation) reactions""" self.loadDatabase(only_families=['Birad_recombination']) for smile in ['C1CCCCC1', 'CCCCCCCCC1C(c2ccccc2)C(CCCCCC)C=CC1c1ccccc1', 'C(=CC(c1ccccc1)C([CH]CCCCCC)C=Cc1ccccc1)[CH]CCCCCC', 'C1(C(CCCCCCCC)C(C(CCCCCC)C=C1)c1ccccc1)c1ccccc1' ]: structure1 = Structure(SMILES=smile) species1 = makeNewSpecies(structure1) print 'Reacting species',species1 # 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 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]
def test22CycloadditionCd(self): """Test 2+2_cycloaddition_Cd reactions""" self.loadDatabase(only_families=['2+2_cycloaddition_Cd']) for smile in [ 'C1(CC(C)(C)O1)(C)C' ]: structure1 = Structure(SMILES=smile) species1 = makeNewSpecies(structure1) print 'Reacting species',species1 # 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 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]
def testDisproportionation(self):
"""A test of a Disproportionation (Radical alpha H abstraction) reactions"""
self.loadDatabase(only_families=['Disproportionation'])
for smile in ['C(=[CH])[CH2]',
]:
structure1 = Structure(SMILES=smile)
species1 = makeNewSpecies(structure1)
print 'Reacting species',species1, 'with itself'
# wipe the reaction list
reaction.reactionDict = {}
rxns = reaction.kineticsDatabase.getReactions([species1,species1])
for rxn in rxns:
print 'Reaction family:',rxn.family
print 'Reaction:',rxn
print 'Kinetics:',rxn.kinetics
print
self.assertTrue(len(rxns)>0,"Didn't make any reactions!")
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),2,"Reaction %s wasn't bimolecular"%rxn)
self.assertEqual(len(rxn.products),2,"Reaction %s wasn't bimolecular"%rxn)
all_products.extend(rxn.products)
print "All products for reacting %s:"%species1, [p.structure[0] for p in all_products]
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 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 testReactionRestart(self):
"""
Restart tests for the :class:`rmg.reaction.Reaction` class.
"""
import rmg.reaction as reaction
import rmg.structure as structure
import rmg.species as species
# Create
smiles = 'C'
struct0 = structure.Structure(SMILES=smiles)
methane, isNew = species.makeNewSpecies(struct0, label=smiles, reactive=True)
reactions = reaction.kineticsDatabase.getReactions([methane])
reaction0 = reactions[0]
# Pickle
f = open('test.pkl', 'wb'); cPickle.dump(reaction0, f); f.close()
# Unpickle
f = open('test.pkl', 'rb'); reaction = cPickle.load(f); f.close()
# Compare
for reactant0 in reaction0.reactants:
match = False
for reactant in reaction.reactants:
if reactant0.isIsomorphic(reactant): match = True
self.assertTrue(match)
for product0 in reaction0.products:
match = False
for product in reaction.products:
if product0.isIsomorphic(product): match = True
self.assertTrue(match)
for kin0 in reaction0.kinetics:
match = False
for kin in reaction.kinetics:
if kin0.equals(kin): match = True
self.assertTrue(match)
self.assertTrue(reaction0.family.label == reaction.family.label)
self.assertTrue(reaction0.atomLabels.keys() == reaction.atomLabels.keys())
self.assertTrue(reaction0.multiplier == reaction.multiplier)
self.assertTrue(reaction0.bestKinetics == reaction.bestKinetics)
def testAllFamilies(self): """A test of all reaction families Doesn't do (m)any actual tests, but hopefully won't cause any errors""" self.loadDatabase() for smile in ['O1OO1', 'C1(CC(C)(C)O1)(C)C', 'C1(C(CCCCCCCC)C(C(CCCCCC)C=C1)c1ccccc1)c1ccccc1', 'C(C)(C)(C)C(=O)OCC(C)C']: structure1 = Structure(SMILES=smile) species1 = makeNewSpecies(structure1) print 'Reacting species',species1 # wipe the reaction list reaction.reactionList=[] rxns = reaction.kineticsDatabase.getReactions([species1]) all_products = [] for rxn in rxns: all_products.extend(rxn.products) print "All products for reacting %s:"%species1, [p.structure[0] for p in all_products]
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)
