def test_create_ports_dict():
doc = create_port_doc()
model = doc.getModel()
comp.create_ports(
model,
portType=comp.PORT_TYPE_PORT,
idRefs={
"extern_port": "extern",
"A_port": "A",
"C_port": "C",
"EX_A_port": "EX_A",
"EX_C_port": "EX_C",
},
)
comp_model = model.getPlugin("comp")
ports = comp_model.getListOfPorts()
assert ports is not None
assert comp_model.getNumPorts() == 5
assert comp_model.getPort("extern_port")
assert comp_model.getPort("A_port")
assert comp_model.getPort("C_port")
assert comp_model.getPort("EX_A_port")
assert comp_model.getPort("EX_C_port")
assert comp_model.getPort("test") is None
def create_dfba_species(model, model_fba, compartment_id, hasOnlySubstanceUnits=False, unit_amount=None, create_port=True,
exclude_sids=[]):
""" Add DFBA species and compartments from fba model to model.
Creates the dynamic species and respetive compartments with
the necessary ports.
This is used in the bounds submodel, update submodel and the
and top model.
:param model:
:param model_fba:
:return:
"""
objects = []
port_sids = []
ex_rids = utils.find_exchange_reactions(model_fba)
for ex_rid in ex_rids:
r = model_fba.getReaction(ex_rid)
sid = r.getReactant(0).getSpecies()
if sid in exclude_sids:
continue
s = model_fba.getSpecies(sid)
# exchange species to create
objects.append(
fac.Species(sid=sid, name=s.getName(), initialConcentration=1.0, substanceUnit=unit_amount,
hasOnlySubstanceUnits=hasOnlySubstanceUnits, compartment=compartment_id)
)
# port of exchange species
port_sids.append(sid)
fac.create_objects(model, objects)
if create_port:
comp.create_ports(model, idRefs=port_sids)
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 = 'extern'
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=True, create_port=True)
# exchange bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True)
objects = [
# exchange bounds
# FIXME: readout the FBA network bounds
mc.Parameter(sid="lb_default", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True),
# kinetic bound parameter & calculation
mc.Parameter(sid='ub_R1', value=1.0, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000625"),
mc.Parameter(sid='k1', value=-0.2, unit="per_s", name="k1", constant=False),
mc.RateRule(sid="ub_R1", value="k1*ub_R1"),
# bound assignment rules
mc.AssignmentRule(sid="lb_EX_A", value='max(lb_default, -A/dt)'),
mc.AssignmentRule(sid="lb_EX_C", value='max(lb_default, -C/dt)'),
]
mc.create_objects(model, objects)
# ports
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=["ub_R1"])
if annotations:
annotation.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, 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 = 'extern'
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=True, create_port=True)
# exchange bounds
builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True)
objects = [
# exchange bounds
# FIXME: readout the FBA network bounds
mc.Parameter(sid="lb_default", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True),
# kinetic bound parameter & calculation
mc.Parameter(sid='ub_R1', value=1.0, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000625"),
mc.Parameter(sid='k1', value=-0.2, unit="per_s", name="k1", constant=False),
mc.RateRule(sid="ub_R1", value="k1*ub_R1"),
# bound assignment rules
mc.AssignmentRule(sid="lb_EX_A", value='max(lb_default, -A/dt)'),
mc.AssignmentRule(sid="lb_EX_C", value='max(lb_default, -C/dt)'),
]
mc.create_objects(model, objects)
# ports
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=["ub_R1"])
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
def create_exchange_reaction(model, species_id, exchange_type=EXCHANGE, flux_unit=None):
""" Factory method to create exchange reactions for species in the FBA model.
Creates the exchange reaction, the upper and lower bounds,
and the ports.
:param model:
:param species_id:
:param exchange_type:
:param flux_unit:
:return:
"""
if exchange_type not in [EXCHANGE, EXCHANGE_IMPORT, EXCHANGE_EXPORT]:
raise ValueError("Wrong exchange_type: {}".format(exchange_type))
# id (e.g. EX_A)
ex_rid = EXCHANGE_REACTION_PREFIX + species_id
lb_id = LOWER_BOUND_PREFIX + ex_rid
ub_id = UPPER_BOUND_PREFIX + ex_rid
lb_value = LOWER_BOUND_DEFAULT
ub_value = UPPER_BOUND_DEFAULT
if exchange_type == EXCHANGE_IMPORT:
# negative flux through exchange reaction
ub_value = ZERO_BOUND
if exchange_type == EXCHANGE_EXPORT:
lb_value = ZERO_BOUND
parameters = [
fac.Parameter(sid=lb_id,
value=lb_value,
unit=flux_unit, constant=True, sboTerm=FLUX_BOUND_SBO),
fac.Parameter(sid=ub_id,
value=ub_value,
unit=flux_unit, constant=True, sboTerm=FLUX_BOUND_SBO),
]
fac.create_objects(model, parameters)
# exchange reactions are all reversible (it depends on the bounds in which direction they operate)
ex_r = fac.create_reaction(model, rid=ex_rid, reversible=True,
reactants={species_id: 1}, sboTerm=EXCHANGE_REACTION_SBO)
# exchange bounds
fbc.set_flux_bounds(ex_r, lb=lb_id, ub=ub_id)
# create ports
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=[ex_rid, lb_id, ub_id])
return ex_r
def create_dfba_dt(model, step_size=DT_SIM, time_unit=None, create_port=True):
""" Creates the dt parameter in the model.
:param model:
:param create_port:
:param step_size:
:param time_unit:
:return:
"""
objects = [
fac.Parameter(sid=DT_ID, value=step_size, unit=time_unit, constant=True, sboTerm=DT_SBO)
]
fac.create_objects(model, objects)
if create_port:
comp.create_ports(model, idRefs=[DT_ID])
def create_exchange_bounds(model_bounds,
model_fba,
unit_flux=None,
create_ports=True):
""" Creates the exchange reaction flux bounds in the bounds model.
:param model_bounds: the bounds model submodel
:param model_fba: the fba submodel
:param unit_flux: unit of fluxes
:param create_ports: should ports be created.
:return:
"""
ex_rids = utils.find_exchange_reactions(model_fba)
objects = []
port_sids = []
for ex_rid, sid in ex_rids.items():
r = model_fba.getReaction(ex_rid)
# lower & upper bound parameters
r_fbc = r.getPlugin(SBML_FBC_NAME)
lb_id = r_fbc.getLowerFluxBound()
lb_value = model_fba.getParameter(lb_id).getValue()
ub_id = r_fbc.getUpperFluxBound()
ub_value = model_fba.getParameter(ub_id).getValue()
# This creates the dynamical flux bound variables which are initialized with the
# constant fba bounds
objects.extend([
# for assignments
Parameter(sid=lb_id,
value=lb_value,
unit=unit_flux,
constant=False,
sboTerm=FLUX_BOUND_SBO),
Parameter(sid=ub_id,
value=ub_value,
unit=unit_flux,
constant=False,
sboTerm=FLUX_BOUND_SBO),
])
port_sids.extend([lb_id, ub_id])
# create bounds
factory.create_objects(model_bounds, objects)
# create ports
if create_ports:
comp.create_ports(model_bounds, idRefs=port_sids)
def test_create_ports_list():
doc = create_port_doc()
model = doc.getModel()
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=["extern", "A", "C", "EX_A", "EX_C"])
comp_model = model.getPlugin("comp")
ports = comp_model.getListOfPorts()
assert ports is not None
assert comp_model.getNumPorts() == 5
assert comp_model.getPort("extern_port")
assert comp_model.getPort("A_port")
assert comp_model.getPort("C_port")
assert comp_model.getPort("EX_A_port")
assert comp_model.getPort("EX_C_port")
assert comp_model.getPort("test") is None
def create_dfba_compartment(model, compartment_id, unit_volume=None, create_port=True):
""" Creates the main compartment for the dynamic species.
:param model:
:param compartment_id: id
:param unit_volume: unit
:param create_port: flag to create port
:return: created libsbml.Compartment
"""
objects = [
fac.Compartment(sid=compartment_id, value=1.0, unit=unit_volume, constant=True, name=compartment_id,
spatialDimensions=3),
]
c = fac.create_objects(model, objects)
if create_port:
comp.create_ports(model, idRefs=[compartment_id])
return c
def create_biomass_species(model, sid, unit, cf_unit, compartment_id, create_port=True):
""" Creates the biomass species.
:param model:
:return:
"""
# FIXME: implement
raise NotImplementedError
pass
fac.create_objects(model, [
fac.Parameter(sid='cf_X', value=1.0, unit="g_per_mmol", name="biomass conversion factor", constant=True),
fac.Species(sid='X', value=0.001, compartment='c', name='biomass', substanceUnit='g', hasOnlySubstanceUnits=True,
conversionFactor='cf_biomass')
])
if create_port:
comp.create_ports(model, idRefs=['X'])
def test_create_ports_list() -> None:
doc: libsbml.SBMLDocument = create_port_doc()
model = doc.getModel()
comp.create_ports(
model, portType=comp.PORT_TYPE_PORT, idRefs=["extern", "A", "C", "EX_A", "EX_C"]
)
comp_model = model.getPlugin("comp")
ports = comp_model.getListOfPorts()
assert ports is not None
assert comp_model.getNumPorts() == 5
assert comp_model.getPort("extern_port")
assert comp_model.getPort("A_port")
assert comp_model.getPort("C_port")
assert comp_model.getPort("EX_A_port")
assert comp_model.getPort("EX_C_port")
assert comp_model.getPort("test") is None
def create_update_parameter(model, sid, unit_flux):
""" Creates the update parameter.
The update parameter correspond to the flux parameters
in the top model.
:param model:
:type model:
:param sid:
:type sid:
:param unit_flux:
:type unit_flux:
:return:
:rtype:
"""
pid = FLUX_PARAMETER_PREFIX + sid
parameter = fac.Parameter(sid=pid, value=1.0, constant=True, unit=unit_flux, sboTerm=UPDATE_PARAMETER_SBO)
fac.create_objects(model, [parameter])
# create port
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=[pid])
return pid
def create_exchange_bounds(model_bounds, model_fba, unit_flux=None, create_ports=True):
""" Creates the exchange reaction flux bounds in the bounds model.
:param model_bounds: the bounds model submodel
:param model_fba: the fba submodel
:param unit_flux: unit of fluxes
:param create_ports: should ports be created.
:return:
"""
ex_rids = utils.find_exchange_reactions(model_fba)
objects = []
port_sids = []
for ex_rid, sid in ex_rids.items():
r = model_fba.getReaction(ex_rid)
# lower & upper bound parameters
r_fbc = r.getPlugin(SBML_FBC_NAME)
lb_id = r_fbc.getLowerFluxBound()
lb_value = model_fba.getParameter(lb_id).getValue()
ub_id = r_fbc.getUpperFluxBound()
ub_value = model_fba.getParameter(ub_id).getValue()
# This creates the dynamical flux bound variables which are initialized with the
# constant fba bounds
objects.extend([
# for assignments
fac.Parameter(sid=lb_id, value=lb_value, unit=unit_flux, constant=False, sboTerm=FLUX_BOUND_SBO),
fac.Parameter(sid=ub_id, value=ub_value, unit=unit_flux, constant=False, sboTerm=FLUX_BOUND_SBO),
])
port_sids.extend([lb_id, ub_id])
# create bounds
fac.create_objects(model_bounds, objects)
# create ports
if create_ports:
comp.create_ports(model_bounds, idRefs=port_sids)
def update_exchange_reactions(model, flux_unit):
""" Updates existing exchange reaction in FBA model.
Sets all the necessary information and checks that correct.
This is mainly used to prepare the exchange reactions of metabolites.
:param flux_unit:
:param model:
:return:
"""
# mapping of bounds to reactions
bounds_dict = dict()
ex_rids = utils.find_exchange_reactions(model)
for ex_rid in ex_rids:
r = model.getReaction(ex_rid)
# make reversible
if not r.getReversible():
r.setReversible(True)
logging.info("Exchange reaction set reversible: {}".format(
r.getId()))
# fix ids for exchange reactions
sref = r.getReactant(0)
sid = sref.getSpecies()
rid = r.getId()
if rid != EXCHANGE_REACTION_PREFIX + sid:
r.setId(EXCHANGE_REACTION_PREFIX + sid)
logging.warning("Exchange reaction fixd id: {} -> {}".format(
rid, EXCHANGE_REACTION_PREFIX + sid))
# new lookup necessary, due to possible changed ids
ex_rids = utils.find_exchange_reactions(model)
for ex_rid in ex_rids:
r = model.getReaction(ex_rid)
fbc_r = r.getPlugin(SBML_FBC_NAME)
# store bounds in dictionary for value lookup
for f_bound in ["getLowerFluxBound", "getUpperFluxBound"]:
bound_id = getattr(fbc_r, f_bound).__call__()
bound = model.getParameter(bound_id)
bounds_dict[bound_id] = bound.getValue()
# create unique bounds for exchange reactions
for ex_rid in ex_rids:
r = model.getReaction(ex_rid)
fbc_r = r.getPlugin(SBML_FBC_NAME)
lb_value = model.getParameter(fbc_r.getLowerFluxBound()).getValue()
ub_value = model.getParameter(fbc_r.getUpperFluxBound()).getValue()
lb_id = LOWER_BOUND_PREFIX + ex_rid
ub_id = UPPER_BOUND_PREFIX + ex_rid
parameters = [
Parameter(sid=lb_id,
value=lb_value,
unit=flux_unit,
constant=True,
sboTerm=FLUX_BOUND_SBO),
Parameter(sid=ub_id,
value=ub_value,
unit=flux_unit,
constant=True,
sboTerm=FLUX_BOUND_SBO),
]
factory.create_objects(model, parameters)
# set bounds
fbc.set_flux_bounds(r, lb=lb_id, ub=ub_id)
# create ports for bounds and reaction
comp.create_ports(model,
portType=comp.PORT_TYPE_PORT,
idRefs=[ex_rid, lb_id, ub_id])
# check all the exchange reactions
for ex_rid in ex_rids:
check_exchange_reaction(model, ex_rid)
def fba_model(sbml_file, directory, annotations=None):
""" FBA model
:param sbml_file: output file name
:param directory: output directory
:return: SBMLDocument
"""
fba_notes = notes.format("""
<h2>FBA submodel</h2>
<p>DFBA fba submodel. Unbalanced metabolites are encoded via exchange fluxes.</p>
""")
doc = builder.template_doc_fba(settings.MODEL_ID)
model = doc.getModel()
utils.set_model_info(model,
notes=fba_notes,
creators=creators,
units=units, main_units=main_units)
objects = [
# compartments
mc.Compartment(sid='extern', value=1.0, unit=UNIT_VOLUME, constant=True, name='external compartment',
spatialDimensions=3),
mc.Compartment(sid='cell', value=1.0, unit=UNIT_VOLUME, constant=True, name='cell', spatialDimensions=3),
mc.Compartment(sid='membrane', value=1.0, unit=UNIT_AREA, constant=True, name='membrane', spatialDimensions=2),
# exchange species
mc.Species(sid='A', name="A", initialConcentration=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
mc.Species(sid='C', name="C", initialConcentration=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
# internal species
mc.Species(sid='B1', name="B1", initialConcentration=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="cell"),
mc.Species(sid='B2', name="B2", initialConcentration=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="cell"),
# bounds
mc.Parameter(sid="ub_R1", value=1.0, unit=UNIT_FLUX, constant=True, sboTerm=builder.FLUX_BOUND_SBO),
mc.Parameter(sid="zero", value=0.0, unit=UNIT_FLUX, constant=True, sboTerm=builder.FLUX_BOUND_SBO),
mc.Parameter(sid="ub_default", value=builder.UPPER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True,
sboTerm=builder.FLUX_BOUND_SBO),
]
mc.create_objects(model, objects)
# reactions
r1 = mc.create_reaction(model, rid="R1", name="A import (R1)", fast=False, reversible=True,
reactants={"A": 1}, products={"B1": 1}, compartment='membrane')
r2 = mc.create_reaction(model, rid="R2", name="B1 <-> B2 (R2)", fast=False, reversible=True,
reactants={"B1": 1}, products={"B2": 1}, compartment='cell')
r3 = mc.create_reaction(model, rid="R3", name="B2 export (R3)", fast=False, reversible=True,
reactants={"B2": 1}, products={"C": 1}, compartment='membrane')
# flux bounds
fbc.set_flux_bounds(r1, lb="zero", ub="ub_R1")
fbc.set_flux_bounds(r2, lb="zero", ub="ub_default")
fbc.set_flux_bounds(r3, lb="zero", ub="ub_default")
# exchange reactions
builder.create_exchange_reaction(model, species_id="A", flux_unit=UNIT_FLUX)
builder.create_exchange_reaction(model, species_id="C", flux_unit=UNIT_FLUX)
# objective function
model_fbc = model.getPlugin("fbc")
fbc.create_objective(model_fbc, oid="R3_maximize", otype="maximize",
fluxObjectives={"R3": 1.0}, active=True)
# create ports for kinetic bounds
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=["ub_R1"])
# write SBML
if annotations:
annotation.annotate_sbml_doc(doc, annotations)
sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
return doc
def fba_model(sbml_file, directory, annotations=None):
""" FBA model
:param sbml_file: output file name
:param directory: output directory
:return: SBMLDocument
"""
fba_notes = notes.format("""
<h2>FBA submodel</h2>
<p>DFBA fba submodel. Unbalanced metabolites are encoded via exchange fluxes.</p>
""")
doc = builder.template_doc_fba(settings.MODEL_ID)
model = doc.getModel()
utils.set_model_info(model,
notes=fba_notes,
creators=creators,
units=units,
main_units=main_units)
objects = [
# compartments
mc.Compartment(sid='extern',
value=1.0,
unit=UNIT_VOLUME,
constant=True,
name='external compartment',
spatialDimensions=3),
mc.Compartment(sid='cell',
value=1.0,
unit=UNIT_VOLUME,
constant=True,
name='cell',
spatialDimensions=3),
mc.Compartment(sid='membrane',
value=1.0,
unit=UNIT_AREA,
constant=True,
name='membrane',
spatialDimensions=2),
# exchange species
mc.Species(sid='A',
name="A",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=True,
compartment="extern"),
mc.Species(sid='C',
name="C",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=True,
compartment="extern"),
# internal species
mc.Species(sid='B1',
name="B1",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=True,
compartment="cell"),
mc.Species(sid='B2',
name="B2",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=True,
compartment="cell"),
# bounds
mc.Parameter(sid="ub_R1",
value=1.0,
unit=UNIT_FLUX,
constant=True,
sboTerm=builder.FLUX_BOUND_SBO),
mc.Parameter(sid="zero",
value=0.0,
unit=UNIT_FLUX,
constant=True,
sboTerm=builder.FLUX_BOUND_SBO),
mc.Parameter(sid="ub_default",
value=builder.UPPER_BOUND_DEFAULT,
unit=UNIT_FLUX,
constant=True,
sboTerm=builder.FLUX_BOUND_SBO),
]
mc.create_objects(model, objects)
# reactions
r1 = mc.create_reaction(model,
rid="R1",
name="A import (R1)",
fast=False,
reversible=True,
reactants={"A": 1},
products={"B1": 1},
compartment='membrane')
r2 = mc.create_reaction(model,
rid="R2",
name="B1 <-> B2 (R2)",
fast=False,
reversible=True,
reactants={"B1": 1},
products={"B2": 1},
compartment='cell')
r3 = mc.create_reaction(model,
rid="R3",
name="B2 export (R3)",
fast=False,
reversible=True,
reactants={"B2": 1},
products={"C": 1},
compartment='membrane')
# flux bounds
fbc.set_flux_bounds(r1, lb="zero", ub="ub_R1")
fbc.set_flux_bounds(r2, lb="zero", ub="ub_default")
fbc.set_flux_bounds(r3, lb="zero", ub="ub_default")
# exchange reactions
builder.create_exchange_reaction(model,
species_id="A",
flux_unit=UNIT_FLUX)
builder.create_exchange_reaction(model,
species_id="C",
flux_unit=UNIT_FLUX)
# objective function
model_fbc = model.getPlugin("fbc")
fbc.create_objective(model_fbc,
oid="R3_maximize",
otype="maximize",
fluxObjectives={"R3": 1.0},
active=True)
# create ports for kinetic bounds
comp.create_ports(model, portType=comp.PORT_TYPE_PORT, idRefs=["ub_R1"])
# write SBML
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
sbml.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
return doc
def update_exchange_reactions(model, flux_unit):
""" Updates existing exchange reaction in FBA model.
Sets all the necessary information and checks that correct.
This is mainly used to prepare the exchange reactions of metabolites.
:param flux_unit:
:param model:
:return:
"""
# mapping of bounds to reactions
bounds_dict = dict()
ex_rids = utils.find_exchange_reactions(model)
for ex_rid in ex_rids:
r = model.getReaction(ex_rid)
# make reversible
if not r.getReversible():
r.setReversible(True)
logging.info("Exchange reaction set reversible: {}".format(r.getId()))
# fix ids for exchange reactions
sref = r.getReactant(0)
sid = sref.getSpecies()
rid = r.getId()
if rid != EXCHANGE_REACTION_PREFIX + sid:
r.setId(EXCHANGE_REACTION_PREFIX + sid)
logging.warning("Exchange reaction fixd id: {} -> {}".format(rid, EXCHANGE_REACTION_PREFIX + sid))
# new lookup necessary, due to possible changed ids
ex_rids = utils.find_exchange_reactions(model)
for ex_rid in ex_rids:
r = model.getReaction(ex_rid)
fbc_r = r.getPlugin(SBML_FBC_NAME)
# store bounds in dictionary for value lookup
for f_bound in ["getLowerFluxBound", "getUpperFluxBound"]:
bound_id = getattr(fbc_r, f_bound).__call__()
bound = model.getParameter(bound_id)
bounds_dict[bound_id] = bound.getValue()
# create unique bounds for exchange reactions
for ex_rid in ex_rids:
r = model.getReaction(ex_rid)
fbc_r = r.getPlugin(SBML_FBC_NAME)
lb_value = model.getParameter(fbc_r.getLowerFluxBound()).getValue()
ub_value = model.getParameter(fbc_r.getUpperFluxBound()).getValue()
lb_id = LOWER_BOUND_PREFIX + ex_rid
ub_id = UPPER_BOUND_PREFIX + ex_rid
parameters = [
fac.Parameter(sid=lb_id,
value=lb_value,
unit=flux_unit, constant=True, sboTerm=FLUX_BOUND_SBO),
fac.Parameter(sid=ub_id,
value=ub_value,
unit=flux_unit, constant=True, sboTerm=FLUX_BOUND_SBO),
]
fac.create_objects(model, parameters)
# set bounds
fbc.set_flux_bounds(r, lb=lb_id, ub=ub_id)
# create ports for bounds and reaction
comp.create_ports(model, portType=comp.PORT_TYPE_PORT,
idRefs=[ex_rid, lb_id, ub_id])
# check all the exchange reactions
for ex_rid in ex_rids:
check_exchange_reaction(model, ex_rid)
