widget4.py 文件源码

def createEXmodel(EXreactions): 
    '''
    This function takes the list of exchange reactions created using the function totalEXRxns and creates a Model object using cobrapy composed of those reactions with the upper bound flux values of 1000, lower bound flux values of -1000, and objective coefficient of 0, and one metabolite as being uptaken by the reaction (stoichiometric coefficient of -1). This is a model composed solely of exchange reactions and it's the model for the extra compartment created for the full community model

    :param EXreactions: list of reactions that are the output of the function totalEXRxns (above)
    :return exchange_model: cobrapy Model object for the compartment that will serve as an extra compartment in the full community model.
    '''


    cherrypy.log("Started the function that creates the exchange reactions for the community model")

    exchange_model = cobra.Model('Model with the exchange reactions only')

    cherrypy.log("Created the base exchange model object")

    for i in EXreactions: 
        new_i = str(i)
        new_i = new_i[3:]
        new_met = cobra.Metabolite(new_i)

        rxn = cobra.Reaction(i)
        rxn.lower_bound = -1000.000
        rxn.upper_bound = 1000.000
        rxn.objective_coefficient = 0.000
        rxn.add_metabolites({new_met:-1.0}) 

        exchange_model.add_reaction(rxn)


    cherrypy.log('Finished adding all exchange reactions in exchange model object. There are %d of them' %(len(exchange_model.reactions)))

    return exchange_model