def loadStates(self, path, statesLibraries=None, depository=True):
"""
Load the RMG states database from the given `path` on disk, where
`path` points to the top-level folder of the RMG states database.
"""
self.states = StatesDatabase()
self.states.load(path, statesLibraries, depository)
def loadOld(self, path):
"""
Load the old RMG database from the given `path` on disk, where `path`
points to the top-level folder of the old RMG database.
"""
self.thermo = ThermoDatabase()
self.thermo.loadOld(path)
self.forbiddenStructures = ForbiddenStructures()
self.forbiddenStructures.loadOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics = KineticsDatabase()
self.kinetics.loadOld(path)
self.states = StatesDatabase()
self.states.loadOld(path)
class RMGDatabase:
"""
The primary class for working with the RMG database.
"""
def __init__(self):
self.thermo = None
self.forbiddenStructures = None
self.kinetics = None
self.states = None
# Store the newly created database in the module.
global database
assert database is None, "Should only make one instance of RMGDatabase because it's stored as a module-level variable."
database = self
def load(self, path, thermoLibraries=None, reactionLibraries=None, seedMechanisms=None, kineticsDepositories=None, statesLibraries=None, depository=True):
"""
Load the RMG database from the given `path` on disk, where `path`
points to the top-level folder of the RMG database. If none of the
optional arguments are provided, then the entire database will be
loaded. You can use the optional arguments to specify that only certain
components of the database be loaded.
"""
self.loadThermo(os.path.join(path, 'thermo'), thermoLibraries, depository)
self.loadForbiddenStructures(os.path.join(path, 'forbiddenStructures.py'))
self.loadKinetics(os.path.join(path, 'kinetics'), reactionLibraries, seedMechanisms, kineticsDepositories)
self.loadStates(os.path.join(path, 'states'), statesLibraries, depository)
def loadThermo(self, path, thermoLibraries=None, depository=True):
"""
Load the RMG thermo database from the given `path` on disk, where
`path` points to the top-level folder of the RMG thermo database.
"""
self.thermo = ThermoDatabase()
self.thermo.load(path, thermoLibraries, depository)
def loadForbiddenStructures(self, path):
"""
Load the RMG forbidden structures from the given `path` on disk, where
`path` points to the forbidden structures file.
"""
self.forbiddenStructures = ForbiddenStructures()
self.forbiddenStructures.load(path)
def loadKinetics(self, path, reactionLibraries=None, seedMechanisms=None, kineticsDepositories=None):
"""
Load the RMG kinetics database from the given `path` on disk, where
`path` points to the top-level folder of the RMG kinetics database.
"""
kineticsLibraries = []
if reactionLibraries is not None and seedMechanisms is not None:
kineticsLibraries.extend(seedMechanisms)
kineticsLibraries.extend(reactionLibraries)
elif reactionLibraries is not None and seedMechanisms is None:
kineticsLibraries.extend(reactionLibraries)
elif reactionLibraries is None and seedMechanisms is not None:
kineticsLibraries.extend(seedMechanisms)
else:
kineticsLibraries = None
self.kinetics = KineticsDatabase()
self.kinetics.load(path, libraries=kineticsLibraries, depositories=kineticsDepositories)
def loadStates(self, path, statesLibraries=None, depository=True):
"""
Load the RMG states database from the given `path` on disk, where
`path` points to the top-level folder of the RMG states database.
"""
self.states = StatesDatabase()
self.states.load(path, statesLibraries, depository)
def loadOld(self, path):
"""
Load the old RMG database from the given `path` on disk, where `path`
points to the top-level folder of the old RMG database.
"""
self.thermo = ThermoDatabase()
self.thermo.loadOld(path)
self.forbiddenStructures = ForbiddenStructures()
self.forbiddenStructures.loadOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics = KineticsDatabase()
self.kinetics.loadOld(path)
self.states = StatesDatabase()
self.states.loadOld(path)
def save(self, path):
"""
Save the RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.mkdir(path)
self.forbiddenStructures.save(os.path.join(path, 'forbiddenStructures.py'))
self.thermo.save(os.path.join(path, 'thermo'))
self.kinetics.save(os.path.join(path, 'kinetics'))
self.states.save(os.path.join(path, 'states'))
def saveOld(self, path):
"""
Save the old RMG database to the given `path` on disk.
"""
if not os.path.exists(path): os.mkdir(path)
self.thermo.saveOld(path)
self.forbiddenStructures.saveOld(os.path.join(path, 'ForbiddenStructures.txt'))
self.kinetics.saveOld(path)
self.states.saveOld(path)
