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import os
from IPython.display import display

import rmgpy
from rmgpy.data.rmg import RMGDatabase
from rmgpy.reaction import Reaction
from rmgpy.molecule.molecule import Molecule
from rmgpy.species import Species
from rmgpy.rmg.react import *


    

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databasePath = os.path.join(rmgpy.settings['test_data.directory'], 'testing_database')

database = RMGDatabase()
database.load(
    path = databasePath,
    thermoLibraries = ['primaryThermoLibrary'],
    reactionLibraries = ['GRI-Mech3.0'],
    seedMechanisms = [],
    kineticsFamilies = 'default',
    )

for family in database.kinetics.families.itervalues():
    family.addKineticsRulesFromTrainingSet(thermoDatabase=database.thermo)
    family.fillKineticsRulesByAveragingUp(verbose=True)


    

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reactants = [
    Species().fromSMILES('[OH]'),
    Species().fromSMILES('O[CH2]'),
]
products = [
    Species().fromSMILES('O'),
    Species().fromSMILES('C=C'),
]
for r in reactants:
    r.generateResonanceIsomers()
for p in products:
    p.generateResonanceIsomers()

rxn = Reaction(reactants=reactants, products=products)


    

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result = reactSpecies(reactants)


    

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for res in result:
    display(res)


    

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rxn0 = result[3]
# for rxn in database.kinetics.libraries['GRI-Mech3.0'].getLibraryReactions():
#     if rxn0.isIsomorphic(rxn):
#         kinetics = rxn.kinetics
#         break
kinetics = database.kinetics.families[rxn0.family].getKinetics(rxn0, templateLabels=rxn0.template, degeneracy=rxn0.degeneracy, returnAllKinetics=False)


    

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kinetics


    

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print kinetics[0].comment


    

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