def LoadAllEstimators():
db_public = SqliteDatabase('../data/public_data.sqlite')
db_gibbs = SqliteDatabase('../res/gibbs.sqlite')
if not db_gibbs.DoesTableExist('prc_pseudoisomers'):
nist_regression = NistRegression(db_gibbs)
nist_regression.Train()
tables = {
'alberty': (db_public, 'alberty_pseudoisomers', 'Alberty'),
'PRC': (db_gibbs, 'prc_pseudoisomers', 'our method (PRC)')
}
estimators = {}
for key, (db, table_name, thermo_name) in tables.iteritems():
if db.DoesTableExist(table_name):
estimators[key] = PsuedoisomerTableThermodynamics.FromDatabase(
db, table_name, name=thermo_name)
else:
logging.warning('The table %s does not exist in %s' %
(table_name, str(db)))
estimators['hatzi_gc'] = Hatzi(use_pKa=False)
#estimators['hatzi_gc_pka'] = Hatzi(use_pKa=True)
if db.DoesTableExist('bgc_pseudoisomers'):
estimators['BGC'] = GroupContribution(db=db_gibbs, transformed=True)
estimators['BGC'].init()
estimators['BGC'].name = 'our method (BGC)'
if db.DoesTableExist('pgc_pseudoisomers'):
estimators['PGC'] = GroupContribution(db=db_gibbs, transformed=False)
estimators['PGC'].init()
estimators['PGC'].name = 'our method (PGC)'
estimators['UGC'] = UnifiedGroupContribution(db=db_gibbs)
estimators['UGC'].init()
estimators['UGC'].name = 'our method (UGC)'
estimators['C1'] = ReactionThermodynamics.FromCsv(
'../data/thermodynamics/c1_reaction_thermodynamics.csv',
estimators['alberty'])
if 'PGC' in estimators:
estimators['merged'] = BinaryThermodynamics(estimators['alberty'],
estimators['PGC'])
estimators['merged_C1'] = BinaryThermodynamics(estimators['C1'],
estimators['PGC'])
for thermo in estimators.values():
thermo.load_bounds('../data/thermodynamics/concentration_bounds.csv')
return estimators
def LoadAllEstimators():
db_public = SqliteDatabase('../data/public_data.sqlite')
db_gibbs = SqliteDatabase('../res/gibbs.sqlite')
if not db_gibbs.DoesTableExist('prc_pseudoisomers'):
nist_regression = NistRegression(db_gibbs)
nist_regression.Train()
tables = {'alberty': (db_public, 'alberty_pseudoisomers', 'Alberty'),
'PRC': (db_gibbs, 'prc_pseudoisomers', 'our method (PRC)')}
estimators = {}
for key, (db, table_name, thermo_name) in tables.iteritems():
if db.DoesTableExist(table_name):
estimators[key] = PsuedoisomerTableThermodynamics.FromDatabase(
db, table_name, name=thermo_name)
else:
logging.warning('The table %s does not exist in %s' % (table_name, str(db)))
estimators['hatzi_gc'] = Hatzi(use_pKa=False)
#estimators['hatzi_gc_pka'] = Hatzi(use_pKa=True)
if db.DoesTableExist('bgc_pseudoisomers'):
estimators['BGC'] = GroupContribution(db=db_gibbs, transformed=True)
estimators['BGC'].init()
estimators['BGC'].name = 'our method (BGC)'
if db.DoesTableExist('pgc_pseudoisomers'):
estimators['PGC'] = GroupContribution(db=db_gibbs, transformed=False)
estimators['PGC'].init()
estimators['PGC'].name = 'our method (PGC)'
estimators['UGC'] = UnifiedGroupContribution(db=db_gibbs)
estimators['UGC'].init()
estimators['UGC'].name = 'our method (UGC)'
estimators['C1'] = ReactionThermodynamics.FromCsv(
'../data/thermodynamics/c1_reaction_thermodynamics.csv',
estimators['alberty'])
if 'PGC' in estimators:
estimators['merged'] = BinaryThermodynamics(estimators['alberty'],
estimators['PGC'])
estimators['merged_C1'] = BinaryThermodynamics(estimators['C1'],
estimators['PGC'])
for thermo in estimators.values():
thermo.load_bounds('../data/thermodynamics/concentration_bounds.csv')
return estimators
dG0_r_prime[0, j] = np.nan
return dG0_r_prime
if __name__ == "__main__":
from pygibbs.groups import GroupContribution
db_public = SqliteDatabase('../data/public_data.sqlite')
db_gibbs = SqliteDatabase('../res/gibbs.sqlite')
alberty = PsuedoisomerTableThermodynamics.FromDatabase(\
db_public, 'alberty_pseudoisomers', name='alberty')
pgc = GroupContribution(db=db_gibbs, transformed=False)
pgc.init()
pgc.name = "PGC"
merged = BinaryThermodynamics(alberty, pgc)
S = np.matrix([[-1, 1, 0, 0, 0, 0, 0, 0, 0],
[ 0, -1, -1, 1, 0, 0, -1, 1, 1],
[ 0, 0, 0, -1, 1, 1, 0, 0, 0],
[ 0, -1, -1, 0, 1, 1, -1, 1, 1]]).T
cids = [311, 158, 10, 566, 24, 36, 2, 8, 9]
print alberty.GetTransformedFormationEnergies(cids)
print alberty.GetTransfromedReactionEnergies(S, cids)
print pgc.GetTransfromedReactionEnergies(S, cids)
dG0_r_primes = merged.GetTransfromedReactionEnergies(S, cids)
print dG0_r_primes
