def bounds_model(sbml_file, directory, doc_fba, annotations=None):
""""
Bounds model.
"""
bounds_notes = notes.format("""
<h2>BOUNDS submodel</h2>
<p>Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA model.</p>
""")
doc = builder.template_doc_bounds(settings.MODEL_ID)
model = doc.getModel()
utils.set_model_info(model,
notes=bounds_notes,
creators=creators,
units=units,
main_units=main_units)
builder.create_dfba_dt(model,
step_size=DT_SIM,
time_unit=UNIT_TIME,
create_port=True)
# compartment
compartment_id = 'cell'
builder.create_dfba_compartment(model,
compartment_id=compartment_id,
unit_volume=UNIT_VOLUME,
create_port=True)
# species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model,
model_fba,
compartment_id=compartment_id,
unit_amount=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
create_port=True)
# exchange bounds
builder.create_exchange_bounds(model_bounds=model,
model_fba=model_fba,
unit_flux=UNIT_FLUX,
create_ports=True)
builder.create_dynamic_bounds(model_bounds=model,
model_fba=model_fba,
unit_flux=UNIT_FLUX)
# annotations
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
def bounds_model(sbml_file, directory, doc_fba=None):
""""
Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA model.
The units of the exchange fluxes must fit to the transported species.
"""
doc = builder.template_doc_bounds("ecoli")
model = doc.getModel()
bounds_notes = notes.format("""
<h2>BOUNDS submodel</h2>
<p>Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA model.</p>
""")
utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units)
# dt
compartment_id = "bioreactor"
builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=True)
# compartment
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True)
# dynamic species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=True,
exclude_sids=['X'])
# FIXME: define biomass separately, also port needed for biomass
mc.create_objects(model, [
mc.Parameter(sid='cf_X', value=1.0, unit="g_per_mmol", name="biomass conversion factor", constant=True),
mc.Species(sid='X', initialAmount=0.001, compartment=compartment_id, name='biomass', substanceUnit='g', hasOnlySubstanceUnits=True,
conversionFactor='cf_X')
])
# exchange & dynamic bounds
if not biomass_weighting:
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True)
builder.create_dynamic_bounds(model, model_fba, unit_flux=UNIT_FLUX)
else:
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX_PER_G, create_ports=True)
builder.create_dynamic_bounds(model, model_fba, unit_flux=UNIT_FLUX_PER_G)
sbmlio.write_sbml(doc, filepath=pjoin(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba, annotations=None):
""""
Bounds model.
"""
bounds_notes = notes.format("""
<h2>BOUNDS submodel</h2>
<p>Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA model.</p>
""")
doc = builder.template_doc_bounds(settings.MODEL_ID)
model = doc.getModel()
utils.set_model_info(model,
notes=bounds_notes,
creators=creators,
units=units, main_units=main_units)
builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=True)
# compartment
compartment_id = 'cell'
builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True)
# species
model_fba = doc_fba.getModel()
builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT,
hasOnlySubstanceUnits=False, create_port=True)
# exchange bounds
builder.create_exchange_bounds(model_bounds=model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True)
builder.create_dynamic_bounds(model_bounds=model, model_fba=model_fba, unit_flux=UNIT_FLUX)
# annotations
if annotations:
annotation.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)