def loadReaction(label, reactants, products, transitionState, degeneracy=1):
global speciesDict, transitionStateDict, reactionDict
logging.info('Loading reaction %s...' % label)
rxn = Reaction(
reactants=[speciesDict[s] for s in reactants],
products=[speciesDict[s] for s in products],
transitionState=transitionStateDict[transitionState],
)
rxn.degeneracy = degeneracy
reactionDict[label] = rxn
def get_reaction_for_entry(entry, database):
"""
Return a Reaction object for a given entry that uses Species instead of
Molecules (so that we can compute the reaction thermo).
"""
reaction = Reaction(reactants=[], products=[])
for reactant in entry.item.reactants:
reactant.generate_resonance_structures()
reactant.thermo = generate_thermo_data(reactant, database)
reaction.reactants.append(reactant)
for product in entry.item.products:
product.generate_resonance_structures()
product.thermo = generate_thermo_data(product, database)
reaction.products.append(product)
reaction.kinetics = entry.data
reaction.degeneracy = entry.item.degeneracy
return reaction
def getReactionForEntry(entry, database):
"""
Return a Reaction object for a given entry that uses Species instead of
Molecules (so that we can compute the reaction thermo).
"""
reaction = Reaction(reactants=[], products=[])
for molecule in entry.item.reactants:
molecule.makeHydrogensExplicit()
reactant = Species(molecule=[molecule], label=molecule.toSMILES())
reactant.generate_resonance_structures()
reactant.thermo = generateThermoData(reactant, database)
reaction.reactants.append(reactant)
for molecule in entry.item.products:
molecule.makeHydrogensExplicit()
product = Species(molecule=[molecule], label=molecule.toSMILES())
product.generate_resonance_structures()
product.thermo = generateThermoData(product, database)
reaction.products.append(product)
reaction.kinetics = entry.data
reaction.degeneracy = entry.item.degeneracy
return reaction
def getReactionForEntry(entry, database):
"""
Return a Reaction object for a given entry that uses Species instead of
Molecules (so that we can compute the reaction thermo).
"""
reaction = Reaction(reactants=[], products=[])
for molecule in entry.item.reactants:
molecule.makeHydrogensExplicit()
reactant = Species(molecule=[molecule], label=molecule.toSMILES())
reactant.generateResonanceIsomers()
reactant.thermo = generateThermoData(reactant, database)
reaction.reactants.append(reactant)
for molecule in entry.item.products:
molecule.makeHydrogensExplicit()
product = Species(molecule=[molecule], label=molecule.toSMILES())
product.generateResonanceIsomers()
product.thermo = generateThermoData(product, database)
reaction.products.append(product)
reaction.kinetics = entry.data
reaction.degeneracy = entry.item.degeneracy
return reaction
