def setUp(self):
rmg_database = RMGDatabase()
rmg_database.load(
rmgpy.settings['database.directory'],
kinetics_families=[
"R_Addition_MultipleBond",
"H_Abstraction",
"intra_H_migration"
],
transport_libraries=[],
reaction_libraries=[],
seed_mechanisms=[],
thermo_libraries=[
'primaryThermoLibrary',
'thermo_DFT_CCSDTF12_BAC',
'CBS_QB3_1dHR'],
solvation=False,
)
self.rmg_database = rmg_database
ts_database = TransitionStates()
path = os.path.join(autotst.settings["tst_database_path"], "H_Abstraction")
global_context = {'__builtins__': None}
local_context = {'DistanceData': DistanceData}
family = self.rmg_database.kinetics.families["H_Abstraction"]
ts_database.family = family
ts_database.load(path, local_context, global_context)
self.ts_database = ts_database
def set_TS_training_data(self, rmg_database):
"""
Loads Database, sets it as class attribute, sets training_set from database
"""
from autotst.data.base import DistanceData, TransitionStateDepository, TSGroups, TransitionStates
ts_database = TransitionStates()
#path = os.path.join(os.path.expandvars("$RMGpy"), "..", "AutoTST", "database", self.family)
path = self.path
global_context = {'__builtins__': None}
local_context = {'DistanceData': DistanceData}
assert self.family in list(rmg_database.kinetics.families.keys(
)), "{} not found in kinetics families. Could not Load".format(family)
family = rmg_database.kinetics.families[self.family]
ts_database.family = family
ts_database.load(path, local_context, global_context)
self.database = ts_database
# Reaction must be a template reaction... found above
logging.info("Getting Training Data for {}".format(family))
training_data = [
(entry.item, entry.data.distances) for entry in list(
ts_database.depository.entries.values())]
self.training_set = training_data
logging.info("Total Distances Count: {}".format(
len(self.training_set)))
return
def test_load(self):
ts_database = TransitionStates()
path = os.path.join(autotst.settings["tst_database_path"], "H_Abstraction")
global_context = {'__builtins__': None}
local_context = {'DistanceData': DistanceData}
family = self.rmg_database.kinetics.families["H_Abstraction"]
ts_database.family = family
ts_database.load(path, local_context, global_context)
self.assertIsInstance(ts_database.depository, TransitionStateDepository)
self.assertIsInstance(ts_database.groups, TSGroups)
def load_databases(self, force_reload=False):
"""
Load the RMG and AutoTST databases, if they have not already been loaded,
into the class level variables where they are stored.
Variables:
- force_reload (bool):if set to True then forces a reload, even if already loaded.
Returns:
- None
"""
if self.rmg_database and self.ts_databases and not force_reload:
return self.rmg_database, self.ts_databases
rmg_database = RMGDatabase()
database_path = rmgpy.settings['database.directory']
logging.info("Loading RMG database from '{}'".format(database_path))
self.possible_families = [ # These families (and only these) will be loaded from both RMG and AutoTST databases
"R_Addition_MultipleBond", "H_Abstraction", "intra_H_migration"
]
try:
rmg_database.load(
database_path,
kineticsFamilies=self.possible_families,
transportLibraries=[],
reactionLibraries=[],
seedMechanisms=[],
thermoLibraries=[
'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC',
'CBS_QB3_1dHR'
],
solvation=False,
)
except IOError:
logging.info(
"RMG database not found at '{}'. This can occur if a git repository of the database is being"
"used rather than the binary version".format(database_path))
database_path = os.path.join(database_path, 'input')
logging.info(
"Loading RMG database instead from '{}'".format(database_path))
rmg_database.load(
database_path,
kineticsFamilies=self.possible_families,
transportLibraries=[],
reactionLibraries=[],
seedMechanisms=[],
thermoLibraries=[
'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC',
'CBS_QB3_1dHR'
],
solvation=False,
)
self.rmg_database = rmg_database
self.ts_databases = dict()
for reaction_family in self.possible_families:
ts_database = TransitionStates()
path = os.path.join(autotst.settings['tst_database_path'],
reaction_family)
global_context = {'__builtins__': None}
local_context = {'DistanceData': DistanceData}
family = rmg_database.kinetics.families[reaction_family]
ts_database.family = family
ts_database.load(path, local_context, global_context)
self.ts_databases[reaction_family] = ts_database
return self.rmg_database, self.ts_databases