def iBsu1103_compound(model):
set_objective_function(model, 'EX_cpd00029_e')
for exchange in model.exchanges:
exchange.lower_bound = -10.0
get_reaction(model, 'rxn00152').bounds = (0.0, 0.0)
get_reaction(model, 'rxn00173').bounds = (0.0, 0.0)
acetate_rate = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('EX_cpd00029_e', acetate_rate), model, reactions, metabolites
def iOD907_compound(model):
set_objective_function(model, 'EX_C00158_extr')
get_reaction(model, 'EX_C00267_extr').lower_bound = -10.0
get_reaction(model, 'R00355_C3_cyto').bounds = (0.0, 0.0)
get_reaction(model, 'R00344_C3_cyto').bounds = (0.0, 0.0)
get_reaction(model, 'T01268_C4_mito').bounds = (0.0, 0.0)
get_reaction(model, 'R01731_C3_cyto').bounds = (0.0, 0.0)
citrate_rate = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('EX_C00158_extr', citrate_rate), model, reactions, metabolites
def iJO1366_compound(model):
set_objective_function(model, 'EX_ac_LPAREN_e_RPAREN_')
get_reaction(model, 'EX_o2_LPAREN_e_RPAREN_').bounds = (0.0, 0.0)
acetate_rate = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('EX_ac_LPAREN_e_RPAREN_', acetate_rate), model, reactions, metabolites
def iOD907(model):
set_objective_function(model, 'Biomass_cyto')
get_reaction(model, 'EX_C00267_extr').lower_bound = -10.0
growth = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('Biomass_cyto', growth), model, reactions, metabolites
def iTO977(model):
set_objective_function(model, 'CBIOMASS')
get_reaction(model, 'GLCxtI').bounds = (-10.0, 10.0)
growth = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('CBIOMASS', growth), model, reactions, metabolites
def iJO1366(model):
set_objective_function(model, 'Ec_biomass_iJO1366_core_53p95M')
get_reaction(model, 'EX_o2_LPAREN_e_RPAREN_').bounds = (0.0, 0.0)
growth = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('Ec_biomass_iJO1366_core_53p95M', growth), model, reactions, metabolites
def iTO977_compound(model):
set_objective_function(model, 'CO2xtO')
get_reaction(model, 'GLCxtI').bounds = (-10.0, 10.0)
co2_rate = model.optimize().objective_value
reactions = len(model.reactions)
metabolites = len(model.metabolites)
return ('CO2xtO', co2_rate), model, reactions, metabolites
def set_root(self):
"""Setting the root, namely the product metabolite in the reaction provided
If the model doesn't have a single product,
a fictitious metabolite is set as root.
It does not add this fictitious metabolite to the model though
This is controlled in the __verify_reaction_principles__ method"""
if not self.__principles_verified:
self.__verify_reaction_principles()
# setting the root
self.root = Node(identifier=self.__metabolite_id,
name=self.__metabolite_name,
compartment=self.__metabolite_name,
is_reactant=self.__metabolite_is_reactant)
reaction = get_reaction(self.model, self.reaction_id)
# testing first the root reaction
if self.objective_direction == 'maximize':
reaction_flux = simulate_reaction(self.__id, self.model, reaction, True)
self.root.reactions_list = [(reaction, reaction.id, reaction_flux,
list_reactants_ids(self.model, reaction.id),
list_products_ids(self.model, reaction.id),
get_reactants(self.model, reaction.id),
get_products(self.model, reaction.id))]
else:
reaction_flux = simulate_reaction(self.__id, self.model, reaction, False)
self.root.reactions_list = [(reaction, reaction.id, reaction_flux,
list_products_ids(self.model, reaction.id),
list_reactants_ids(self.model, reaction.id),
get_products(self.model, reaction.id),
get_reactants(self.model, reaction.id))]
self.root.analysis = reaction_flux