def clip_prefixes(path_in, path_out):
""" Clips all prefixes in model.
This takes very long.
:param path_in:
:param path_out:
:return:
"""
doc_fba = sbmlio.read_sbml(path_in)
model = doc_fba.getModel()
# clip R_ reaction and M_ metabolite prefixes
utils.clip_prefixes_in_model(model)
sbmlio.write_sbml(doc_fba, filepath=path_out, validate=False)
def clip_prefixes(path_in, path_out):
""" Clips all prefixes in model.
This takes very long.
:param path_in:
:param path_out:
:return:
"""
doc_fba = sbmlio.read_sbml(path_in)
model = doc_fba.getModel()
# clip R_ reaction and M_ metabolite prefixes
utils.clip_prefixes_in_model(model)
sbmlio.write_sbml(doc_fba, filepath=path_out, validate=False)
def fba_model(sbml_file, directory):
""" Create FBA submodel.
"""
# Read the model
fba_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/iAB_RBC_283.xml')
doc_fba = sbmlio.read_sbml(fba_path)
# add comp
doc_fba.enablePackage(
"http://www.sbml.org/sbml/level3/version1/comp/version1", "comp", True)
doc_fba.setPackageRequired("comp", True)
# add notes
model = doc_fba.getModel()
fba_notes = notes.format("""DFBA FBA submodel.""")
utils.set_model_info(model,
notes=fba_notes,
creators=None,
units=units,
main_units=main_units)
# clip R_ reaction and M_ metabolite prefixes
utils.clip_prefixes_in_model(model)
# set id & framework
model.setId('{}_fba'.format(settings.MODEL_ID))
model.setName('{} (FBA)'.format(settings.MODEL_ID))
model.setSBOTerm(comp.SBO_FLUX_BALANCE_FRAMEWORK)
# add units and information
for species in model.getListOfSpecies():
species.setInitialConcentration(0.0)
species.setHasOnlySubstanceUnits(False)
species.setUnits(UNIT_AMOUNT)
for compartment in model.getListOfCompartments():
compartment.setUnits(UNIT_VOLUME)
# update the existing exchange reactions
builder.update_exchange_reactions(model, flux_unit=UNIT_FLUX)
# write SBML file
sbmlio.write_sbml(doc_fba,
filepath=pjoin(directory, sbml_file),
validate=True)
return doc_fba
def fba_model(sbml_file, directory):
""" Create FBA submodel.
"""
# Read the model
fba_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/iAB_RBC_283.xml')
doc_fba = sbmlio.read_sbml(fba_path)
# add comp
doc_fba.enablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1", "comp", True)
doc_fba.setPackageRequired("comp", True)
# add notes
model = doc_fba.getModel()
fba_notes = notes.format("""DFBA FBA submodel.""")
utils.set_model_info(model, notes=fba_notes,
creators=None, units=units, main_units=main_units)
# clip R_ reaction and M_ metabolite prefixes
utils.clip_prefixes_in_model(model)
# set id & framework
model.setId('{}_fba'.format(settings.MODEL_ID))
model.setName('{} (FBA)'.format(settings.MODEL_ID))
model.setSBOTerm(comp.SBO_FLUX_BALANCE_FRAMEWORK)
# add units and information
for species in model.getListOfSpecies():
species.setInitialConcentration(0.0)
species.setHasOnlySubstanceUnits(False)
species.setUnits(UNIT_AMOUNT)
for compartment in model.getListOfCompartments():
compartment.setUnits(UNIT_VOLUME)
# update the existing exchange reactions
builder.update_exchange_reactions(model, flux_unit=UNIT_FLUX)
# write SBML file
sbmlio.write_sbml(doc_fba, filepath=pjoin(directory, sbml_file), validate=True)
return doc_fba
def fba_model(sbml_file, directory):
""" Create FBA submodel.
"""
# Read the model
fba_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/ecoli_fba.xml')
doc_fba = sbml.read_sbml(fba_path)
# add comp
doc_fba.enablePackage(
"http://www.sbml.org/sbml/level3/version1/comp/version1", "comp", True)
doc_fba.setPackageRequired("comp", True)
# add notes
model = doc_fba.getModel()
fba_notes = notes.format("""DFBA FBA submodel.""")
utils.set_model_info(model,
notes=fba_notes,
creators=None,
units=units,
main_units=main_units)
# clip R_ reaction and M_ metabolite prefixes
utils.clip_prefixes_in_model(model)
# set id & framework
model.setId('ecoli_fba')
model.setName('ecoli (FBA)')
model.setSBOTerm(comp.SBO_FLUX_BALANCE_FRAMEWORK)
# add units and information
for species in model.getListOfSpecies():
species.setInitialConcentration(0.0)
species.setHasOnlySubstanceUnits(False)
species.setUnits(UNIT_AMOUNT)
for compartment in model.getListOfCompartments():
compartment.setUnits(UNIT_VOLUME)
# The ATPM (atp maintainance reactions creates many problems in the DFBA)
# mainly resulting in infeasible solutions when some metabolites run out.
# ATP -> ADP is part of the biomass, so we set the lower bound to zero
r_ATPM = model.getReaction('ATPM')
r_ATPM_fbc = r_ATPM.getPlugin(builder.SBML_FBC_NAME)
lb_id = r_ATPM_fbc.getLowerFluxBound()
model.getParameter(lb_id).setValue(0.0) # 8.39 before
# make unique upper and lower bounds for exchange reaction
if not biomass_weighting:
builder.update_exchange_reactions(model=model, flux_unit=UNIT_FLUX)
else:
builder.update_exchange_reactions(model=model,
flux_unit=UNIT_FLUX_PER_G)
# add exchange reaction for biomass (X)
# we are adding the biomass component to the biomass function and create an
# exchange reaction for it
r_biomass = model.getReaction('BIOMASS_Ecoli_core_w_GAM')
# FIXME: refactor in function
# FIXME: annotate biomass species (SBO for biomass missing)
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='c',
name='biomass',
substanceUnit='g',
hasOnlySubstanceUnits=True,
conversionFactor='cf_X')
])
pr_biomass = r_biomass.createProduct()
pr_biomass.setSpecies('X')
pr_biomass.setStoichiometry(1.0)
pr_biomass.setConstant(True)
# FIXME: the flux units must fit to the species units.
if not biomass_weighting:
builder.create_exchange_reaction(model,
species_id='X',
flux_unit=UNIT_FLUX,
exchange_type=builder.EXCHANGE_EXPORT)
else:
builder.create_exchange_reaction(model,
species_id='X',
flux_unit=UNIT_FLUX_PER_G,
exchange_type=builder.EXCHANGE_EXPORT)
# write SBML file
sbml.write_sbml(doc_fba,
filepath=pjoin(directory, sbml_file),
validate=True)
# Set kinetic laws to zero for kinetic simulation
'''
for reaction in model.getListOfReactions():
ast_node = mc.ast_node_from_formula(model=model, formula='0 {}'.format(UNIT_FLUX))
law = reaction.createKineticLaw()
law.setMath(ast_node)
'''
return doc_fba
def fba_model(sbml_file, directory):
""" Create FBA submodel.
"""
# Read the model
fba_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/ecoli_fba.xml')
doc_fba = sbmlio.read_sbml(fba_path)
# add comp
doc_fba.enablePackage("http://www.sbml.org/sbml/level3/version1/comp/version1", "comp", True)
doc_fba.setPackageRequired("comp", True)
# add notes
model = doc_fba.getModel()
fba_notes = notes.format("""DFBA FBA submodel.""")
utils.set_model_info(model, notes=fba_notes,
creators=None, units=units, main_units=main_units)
# clip R_ reaction and M_ metabolite prefixes
utils.clip_prefixes_in_model(model)
# set id & framework
model.setId('ecoli_fba')
model.setName('ecoli (FBA)')
model.setSBOTerm(comp.SBO_FLUX_BALANCE_FRAMEWORK)
# add units and information
for species in model.getListOfSpecies():
species.setInitialConcentration(0.0)
species.setHasOnlySubstanceUnits(False)
species.setUnits(UNIT_AMOUNT)
for compartment in model.getListOfCompartments():
compartment.setUnits(UNIT_VOLUME)
# The ATPM (atp maintainance reactions creates many problems in the DFBA)
# mainly resulting in infeasible solutions when some metabolites run out.
# ATP -> ADP is part of the biomass, so we set the lower bound to zero
r_ATPM = model.getReaction('ATPM')
r_ATPM_fbc = r_ATPM.getPlugin(builder.SBML_FBC_NAME)
lb_id = r_ATPM_fbc.getLowerFluxBound()
model.getParameter(lb_id).setValue(0.0) # 8.39 before
# make unique upper and lower bounds for exchange reaction
if not biomass_weighting:
builder.update_exchange_reactions(model=model, flux_unit=UNIT_FLUX)
else:
builder.update_exchange_reactions(model=model, flux_unit=UNIT_FLUX_PER_G)
# add exchange reaction for biomass (X)
# we are adding the biomass component to the biomass function and create an
# exchange reaction for it
r_biomass = model.getReaction('BIOMASS_Ecoli_core_w_GAM')
# FIXME: refactor in function
# FIXME: annotate biomass species (SBO for biomass missing)
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='c', name='biomass', substanceUnit='g', hasOnlySubstanceUnits=True,
conversionFactor='cf_X')
])
pr_biomass = r_biomass.createProduct()
pr_biomass.setSpecies('X')
pr_biomass.setStoichiometry(1.0)
pr_biomass.setConstant(True)
# FIXME: the flux units must fit to the species units.
if not biomass_weighting:
builder.create_exchange_reaction(model, species_id='X', flux_unit=UNIT_FLUX, exchange_type=builder.EXCHANGE_EXPORT)
else:
builder.create_exchange_reaction(model, species_id='X', flux_unit=UNIT_FLUX_PER_G, exchange_type=builder.EXCHANGE_EXPORT)
# write SBML file
sbmlio.write_sbml(doc_fba, filepath=pjoin(directory, sbml_file), validate=True)
# Set kinetic laws to zero for kinetic simulation
'''
for reaction in model.getListOfReactions():
ast_node = mc.ast_node_from_formula(model=model, formula='0 {}'.format(UNIT_FLUX))
law = reaction.createKineticLaw()
law.setMath(ast_node)
'''
return doc_fba