本文整理汇总了Python中cobra.Model.to_array_based_model方法的典型用法代码示例。如果您正苦于以下问题：Python Model.to_array_based_model方法的具体用法？Python Model.to_array_based_model怎么用？Python Model.to_array_based_model使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类cobra.Model的用法示例。
在下文中一共展示了Model.to_array_based_model方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: print
# 需要导入模块: from cobra import Model [as 别名]
# 或者: from cobra.Model import to_array_based_model [as 别名]
CO2t,
EX_co2,
PDH,
CS,
ACO1,
ACO2,
ICDH1,
ICDH2,
AKGDH,
SCS,
SDH,
FMS,
MDH
])
print 'Reactions'
print '---------'
for reaction in model.reactions:
print('%s : %s' % (reaction.id, reaction.reaction))
print '\nMetabolites'
print '-----------'
for metabolite in model.metabolites:
print('%s : %s' % (metabolite.id, metabolite.formula))
array_model = model.to_array_based_model()
print array_model.S.todense()
for reaction in model.reactions:
print reaction.check_mass_balance()
示例2: setupSimulation
# 需要导入模块: from cobra import Model [as 别名]
# 或者: from cobra.Model import to_array_based_model [as 别名]
def setupSimulation(self):
'''setup reaction participant, enzyme counts matrices'''
Submodel.setupSimulation(self)
'''Setup FBA'''
cobraModel = CobraModel(self.id)
self.cobraModel = cobraModel
#setup metabolites
cbMets = []
for species in self.species:
cbMets.append(CobraMetabolite(id = species.id, name = species.name))
cobraModel.add_metabolites(cbMets)
#setup reactions
for rxn in self.reactions:
cbRxn = CobraReaction(
id = rxn.id,
name = rxn.name,
lower_bound = -self.defaultFbaBound if rxn.reversible else 0,
upper_bound = self.defaultFbaBound,
objective_coefficient = 1 if rxn.id == 'MetabolismProduction' else 0,
)
cobraModel.add_reaction(cbRxn)
cbMets = {}
for part in rxn.participants:
cbMets[part.id] = part.coefficient
cbRxn.add_metabolites(cbMets)
#add external exchange reactions
self.exchangedSpecies = []
for species in self.species:
if species.compartment.id == 'e':
cbRxn = CobraReaction(
id = '%sEx' % species.species.id,
name = '%s exchange' % species.species.name,
lower_bound = -self.defaultFbaBound,
upper_bound = self.defaultFbaBound,
objective_coefficient = 0,
)
cobraModel.add_reaction(cbRxn)
cbRxn.add_metabolites({species.id: 1})
self.exchangedSpecies.append(ExchangedSpecies(id = species.id, reactionIndex = cobraModel.reactions.index(cbRxn)))
#add biomass exchange reaction
cbRxn = CobraReaction(
id = 'BiomassEx',
name = 'Biomass exchange',
lower_bound = 0,
upper_bound = self.defaultFbaBound,
objective_coefficient = 0,
)
cobraModel.add_reaction(cbRxn)
cbRxn.add_metabolites({'Biomass[c]': -1})
'''Bounds'''
#thermodynamic
arrayCobraModel = cobraModel.to_array_based_model()
self.thermodynamicBounds = {
'lower': np.array(arrayCobraModel.lower_bounds.tolist()),
'upper': np.array(arrayCobraModel.upper_bounds.tolist()),
}
#exchange reactions
carbonExRate = self.getComponentById('carbonExchangeRate', self.parameters).value
nonCarbonExRate = self.getComponentById('nonCarbonExchangeRate', self.parameters).value
self.exchangeRateBounds = {
'lower': np.full(len(cobraModel.reactions), -np.nan),
'upper': np.full(len(cobraModel.reactions), np.nan),
}
for exSpecies in self.exchangedSpecies:
if self.getComponentById(exSpecies.id, self.species).species.containsCarbon():
self.exchangeRateBounds['lower'][exSpecies.reactionIndex] = -carbonExRate
self.exchangeRateBounds['upper'][exSpecies.reactionIndex] = carbonExRate
else:
self.exchangeRateBounds['lower'][exSpecies.reactionIndex] = -nonCarbonExRate
self.exchangeRateBounds['upper'][exSpecies.reactionIndex] = nonCarbonExRate
'''Setup reactions'''
self.metabolismProductionReaction = {
'index': cobraModel.reactions.index(cobraModel.reactions.get_by_id('MetabolismProduction')),
'reaction': self.getComponentById('MetabolismProduction', self.reactions),
}