widget4.py 文件源码

def createReverseEXmodel(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 produced by the reaction (stoichiometric coefficient of 1). This is a model composed solely of exchange reactions. The metabolite information for these reactions will be used to update the metabolites of the exchange reactions for models A and B.

    :param EXreactions: list of reactions that are the output of the function totalEXRxns (above)
    :return exchange_modelRev: cobrapy Model object containing only exchange reactions with the production of their respective metabolites
    '''

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

    exchange_modelRev = cobra.Model('Model with the exchange reactions only with reversed stoi coefficient')

    cherrypy.log("Created the base reverse 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_modelRev.add_reaction(rxn)

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

    return exchange_modelRev