def create_reaction_rule_cache(self, rr):
reactants = [id for id in rr.reactants]
products = [id for id in rr.products]
if len(reactants) == 1:
k = float(rr['k'])
elif len(reactants) == 2:
st1 = self.model.get_species_type_by_id(reactants[0])
st2 = self.model.get_species_type_by_id(reactants[1])
D = float(st1['D']) + float(st2['D'])
sigma = float(st1['radius']) + float(st2['radius'])
kD = utils.k_D(D, sigma)
k = float(rr['k'])
if kD == 0.0:
k = 0.0
elif k != 0.0:
k = utils.k_on(k, kD) * (1000 * utils.N_A)
return ReactionRuleCache(rr, reactants, products, k)
def create_reaction_rule_cache(self, rr):
reactants = [id for id in rr.reactants]
products = [id for id in rr.products]
if len(reactants) == 1:
k = float(rr['k'])
elif len(reactants) == 2:
st1 = self.model.get_species_type_by_id(reactants[0])
st2 = self.model.get_species_type_by_id(reactants[1])
D = float(st1['D']) + float(st2['D'])
sigma = float(st1['radius']) + float(st2['radius'])
kD = utils.k_D(D, sigma)
k = float(rr['k'])
if kD == 0.0:
k = 0.0
elif k != 0.0:
k = utils.k_on(k, kD) * (1000 * utils.N_A)
return ReactionRuleCache(rr, reactants, products, k)
def create_reaction_rule_cache(self, rr):
reactants = [id for id in rr.reactants]
products = [id for id in rr.products]
k = float(rr.k)
if self.convert_rates == False:
# Don't do the conversion below.
return ReactionRuleCache(rr, reactants, products, k)
if len(reactants) == 1:
if len(products) == 2:
st1 = self.model.get_species_type_by_id(products[0])
st2 = self.model.get_species_type_by_id(products[1])
# Lookup kon for reverse reaction rule.
for rr_possible_reverse in self.get_reaction_rule2(st1, st2):
if rr_possible_reverse.products == reactants:
rr_reverse = rr_possible_reverse
kon = float(rr_reverse.k)
# Compute kD for reverse reaction.
D = float(st1['D']) + float(st2['D'])
sigma = float(st1['radius']) + float(st2['radius'])
kD = utils.k_D(D, sigma)
# Use overall rate internally.
k = utils.k_off(k, kon, kD)
elif len(reactants) == 2:
st1 = self.model.get_species_type_by_id(reactants[0])
st2 = self.model.get_species_type_by_id(reactants[1])
D = float(st1['D']) + float(st2['D'])
sigma = float(st1['radius']) + float(st2['radius'])
kD = utils.k_D(D, sigma)
if kD == 0.0:
k = 0.0
elif k != 0.0:
# Use overall rate kon internally.
k = utils.k_on(k, kD)
return ReactionRuleCache(rr, reactants, products, k)
def create_reaction_rule_cache(self, rr):
reactants = [id for id in rr.reactants]
products = [id for id in rr.products]
k = float(rr.k)
if self.convert_rates == False:
# Don't do the conversion below.
return ReactionRuleCache(rr, reactants, products, k)
if len(reactants) == 1:
if len(products) == 2:
st1 = self.model.get_species_type_by_id(products[0])
st2 = self.model.get_species_type_by_id(products[1])
# Lookup kon for reverse reaction rule.
for rr_possible_reverse in self.get_reaction_rule2(st1, st2):
if rr_possible_reverse.products == reactants:
rr_reverse = rr_possible_reverse
kon = float(rr_reverse.k)
# Compute kD for reverse reaction.
D = float(st1['D']) + float(st2['D'])
sigma = float(st1['radius']) + float(st2['radius'])
kD = utils.k_D(D, sigma)
# Use overall rate internally.
k = utils.k_off(k, kon, kD)
elif len(reactants) == 2:
st1 = self.model.get_species_type_by_id(reactants[0])
st2 = self.model.get_species_type_by_id(reactants[1])
D = float(st1['D']) + float(st2['D'])
sigma = float(st1['radius']) + float(st2['radius'])
kD = utils.k_D(D, sigma)
if kD == 0.0:
k = 0.0
elif k != 0.0:
# Use overall rate kon internally.
k = utils.k_on(k, kD)
return ReactionRuleCache(rr, reactants, products, k)