def testGetRingGroupsFromComments(self):
"""
Test that getRingGroupsFromComments method works for fused polycyclics.
"""
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'))
smi = 'C12C(C3CCC2C3)C4CCC1C4'#two norbornane rings fused together
spc = Species().fromSMILES(smi)
spc.generateThermoData(rmg.database)
thermodb = rmg.database.thermo
thermodb.getRingGroupsFromComments(spc.thermo)
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
def testGetRingGroupsFromComments(self):
"""
Test that getRingGroupsFromComments method works for fused polycyclics.
"""
# set-up RMG object
rmg = RMG()
# load kinetic database and forbidden structures
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
# forbidden structure loading
rmg.database.loadThermo(os.path.join(path, 'thermo'))
smi = 'C12C(C3CCC2C3)C4CCC1C4' #two norbornane rings fused together
spc = Species().fromSMILES(smi)
spc.generateThermoData(rmg.database)
thermodb = rmg.database.thermo
thermodb.getRingGroupsFromComments(spc.thermo)
import rmgpy.data.rmg
rmgpy.data.rmg.database = None
print 'Loading {0} library'.format(libraryName)
kineticLibrary = database.kinetics.libraries[libraryName]
reactionList = []
for index, entry in kineticLibrary.entries.iteritems():
reaction = entry.item
reaction.kinetics = entry.data
reactionList.append(reaction)
speciesList = []
index = 0
for spec in kineticLibrary.getSpecies().values():
index = index + 1
species = Species(molecule = spec.molecule)
species.generateThermoData(database)
species.index = index
speciesList.append(species)
for reaction in reactionList:
for reactant in reaction.reactants:
for spec in speciesList:
if reactant.isIsomorphic(spec):
reactant.index = spec.index
spec.label = reactant.label
for product in reaction.products:
for spec in speciesList:
if product.isIsomorphic(spec):
product.index = spec.index
spec.label = product.label
reactionList = []
for index, entry in kineticLibrary.entries.iteritems():
reaction = entry.item
reaction.kinetics = entry.data
reactionList.append(reaction)
speciesList = []
index = 0
speciesDict = kineticLibrary.getSpecies(
os.path.join(settings['database.directory'], 'kinetics', 'libraries',
libraryName, 'dictionary.txt'))
for spec in speciesDict.values():
index = index + 1
species = Species(molecule=spec.molecule)
species.generateThermoData(database)
species.index = index
speciesList.append(species)
for reaction in reactionList:
for reactant in reaction.reactants:
for spec in speciesList:
if reactant.isIsomorphic(spec):
reactant.index = spec.index
spec.label = reactant.label
for product in reaction.products:
for spec in speciesList:
if product.isIsomorphic(spec):
product.index = spec.index
spec.label = product.label