In [1]:

    

import logging


    

In [2]:

    

logger = logging.getLogger("")


    

In [3]:

    

logger.setLevel(logging.DEBUG)


    

In [4]:

    

import pyorganism


    

In [5]:

    

import pyorganism.metabolism as pymet


    

    




/home/moritz/.virtualenvs/control/local/lib/python2.7/site-packages/pyorganism/metabolism/__init__.py:44: UserWarning: You do not have the required SOAPpy package: KEGG interface            is disabled.
  is disabled.")

In [6]:

    

options = pyorganism.OptionsManager.get_instance()


    

In [7]:

    

options.compartment_suffixes = {"Exchange": "_b", "C_c": "_c", "C_e": "_e"}


    

In [8]:

    

parser = pymet.SBMLParser()


    

In [9]:

    

met = parser("Ecoli_core.xml")


    

    




INFO:pyorganism.io.sbml:2 compartments
INFO:pyorganism.io.sbml:92 (compartmentalized) compounds
INFO:pyorganism.io.sbml:95 reactions

In [10]:

    

for comp in met.compartments:
    print str(comp), comp.name, len(comp)


    

    




C_c Cytosol 52
EX Exchange 20
C_e Extraorganism 20

In [11]:

    

(model, known_fluxes) = pymet.generate_fba_model(met, "core", fluxes=True)


    

In [12]:

    

exchange = pymet.SBMLCompartment["EX"]


    

In [13]:

    

for cmpd in exchange.iter_compartmentalized():
    logger.info(str(cmpd))
    model.add_source(cmpd, ub=1000)
    model.add_drain(cmpd, ub=1000)


    

    




INFO:root:glu-L_b
INFO:root:pyr_b
INFO:root:h_b
INFO:root:nh4_b
INFO:root:acald_b
INFO:root:o2_b
INFO:root:fru_b
INFO:root:mal-L_b
INFO:root:lac-D_b
INFO:root:fum_b
INFO:root:succ_b
INFO:root:for_b
INFO:root:gln-L_b
INFO:root:pi_b
INFO:root:co2_b
INFO:root:glc-D_b
INFO:root:ac_b
INFO:root:h2o_b
INFO:root:etoh_b
INFO:root:akg_b

In [14]:

    

model.fba()


    

In [15]:

    

model.get_objective_value()


    

    
Out[15]:





0.8739215069503519