def testInitialSpecies(self):
" Test we can check whether the solvent is listed as one of the initial species in various scenarios "
# Case 1. when SMILES for solvent is available, the molecular structures of the initial species and the solvent
# are compared to check whether the solvent is in the initial species list
# Case 1-1: the solvent water is not in the initialSpecies list, so it raises Exception
rmg=RMG()
rmg.initialSpecies = []
solute = Species(label='n-octane', molecule=[Molecule().fromSMILES('C(CCCCC)CC')])
rmg.initialSpecies.append(solute)
rmg.solvent = 'water'
solventStructure = Species().fromSMILES('O')
self.assertRaises(Exception, self.database.checkSolventinInitialSpecies, rmg, solventStructure)
# Case 1-2: the solvent is now octane and it is listed as the initialSpecies. Although the string
# names of the solute and the solvent are different, because the solvent SMILES is provided,
# it can identify the 'n-octane' as the solvent
rmg.solvent = 'octane'
solventStructure = Species().fromSMILES('CCCCCCCC')
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
# Case 2: the solvent SMILES is not provided. In this case, it can identify the species as the
# solvent by looking at the string name.
# Case 2-1: Since 'n-octane and 'octane' are not equal, it raises Exception
solventStructure = None
self.assertRaises(Exception, self.database.checkSolventinInitialSpecies, rmg, solventStructure)
# Case 2-2: The label 'n-ocatne' is corrected to 'octane', so it is identified as the solvent
rmg.initialSpecies[0].label = 'octane'
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
def testInitialSpecies(self):
" Test we can check whether the solvent is listed as one of the initial species in various scenarios "
# Case 1. when SMILES for solvent is available, the molecular structures of the initial species and the solvent
# are compared to check whether the solvent is in the initial species list
# Case 1-1: the solvent water is not in the initialSpecies list, so it raises Exception
rmg=RMG()
rmg.initialSpecies = []
solute = Species(label='n-octane', molecule=[Molecule().fromSMILES('C(CCCCC)CC')])
rmg.initialSpecies.append(solute)
rmg.solvent = 'water'
solventStructure = Species().fromSMILES('O')
self.assertRaises(Exception, self.database.checkSolventinInitialSpecies, rmg, solventStructure)
# Case 1-2: the solvent is now octane and it is listed as the initialSpecies. Although the string
# names of the solute and the solvent are different, because the solvent SMILES is provided,
# it can identify the 'n-octane' as the solvent
rmg.solvent = 'octane'
solventStructure = Species().fromSMILES('CCCCCCCC')
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
# Case 2: the solvent SMILES is not provided. In this case, it can identify the species as the
# solvent by looking at the string name.
# Case 2-1: Since 'n-octane and 'octane' are not equal, it raises Exception
solventStructure = None
self.assertRaises(Exception, self.database.checkSolventinInitialSpecies, rmg, solventStructure)
# Case 2-2: The label 'n-ocatne' is corrected to 'octane', so it is identified as the solvent
rmg.initialSpecies[0].label = 'octane'
self.database.checkSolventinInitialSpecies(rmg, solventStructure)
self.assertTrue(rmg.initialSpecies[0].isSolvent)
from rmgpy.rmg.model import CoreEdgeReactionModel
from rmgpy.rmg.main import RMG
from rmgpy import settings
from rmgpy.data.rmg import RMGDatabase
rmg = RMG()
rmg.database = RMGDatabase()
path = os.path.join(settings['database.directory'])
rmg.database.loadThermo(os.path.join(path,'thermo'))
mol = Molecule().fromSMILES('C1=CC=CC=C1')
tdt = rmg.database.thermo.estimateThermoViaGroupAdditivity(mol)
print tdt.comment
print mol.isAromatic()
spc = Species().fromSMILES('C1=CC=CC=C1')
tdt = rmg.database.thermo.getThermoDataFromGroups(spc)
print tdt.comment
print '\n'
rmg.reactionModel = CoreEdgeReactionModel()
spc, isNew = rmg.reactionModel.makeNewSpecies(mol)
rmg.reactionModel.addSpeciesToEdge(spc)
rmg.initialSpecies = []
rmg.initialSpecies.append(spc)
for species in rmg.initialSpecies:
#species.generateThermoData(rmg.database, quantumMechanics=rmg.reactionModel.quantumMechanics)
#print species.thermo.comment
tdt = rmg.database.thermo.getThermoDataFromGroups(spc)
print tdt.comment
rmg.scratchDirectory = '.'
rmg.databaseDirectory = databaseDirectory
rmg.thermoLibraries = ['primaryThermoLibrary']
rmg.kineticsFamilies = ['H_Abstraction',]
rmg.reactionLibraries = [('KlippensteinH2O2', False),]
rmgpy.rmg.input.rmg = rmg # put it in this scope so these functions can modify it
#rmg.loadDatabase() # this seems to hang (forever??) but turns out it's not needed!
logging.info("Loaded database.")
# In[4]:
rmg.reactionModel = rmgpy.rmg.model.CoreEdgeReactionModel()
rmg.reactionModel.kineticsEstimator = 'rate rules'
rmg.reactionModel.verboseComments = True
rmg.initialSpecies = []
rmg.reactionSystems = []
def makeOrEmptyDirectory(path):
"""Either create a directory at `path` or delete everything in it if it exists"""
if os.path.exists(path):
assert os.path.isdir(path), "Path {0} exists but is not a directory".format(path)
# empty it out
for root, dirs, files in os.walk(path, topdown=False):
for name in files:
os.remove(os.path.join(root, name))
for name in dirs:
os.rmdir(os.path.join(root, name))
else:
os.makedirs(path)
