"""FBA example with exchange reactions."""
from sbmlutils.examples import templates
from sbmlutils.factory import *
from sbmlutils.metadata import *
[docs]class U(Units):
"""UnitsDefinition."""
[docs] mmole = UnitDefinition("mmole")
[docs] m2 = UnitDefinition("m2", "meter^2")
[docs] hr = UnitDefinition("hr")
[docs] mmole_per_l = UnitDefinition("mmole_per_l", "mmole/liter")
[docs] mmole_per_hr = UnitDefinition("mmole_per_hr", "mmole/hr")
[docs]model = Model(
"fbc_v2",
name="Example FBC v2",
packages=[Package.FBC_V3],
creators=templates.creators,
notes="""
# Model with fbc version 2
Example creating fbc model.
"""
+ templates.terms_of_use,
units=U,
model_units=ModelUnits(
time=U.hr,
extent=U.mmole,
substance=U.mmole,
length=U.meter,
area=U.m2,
volume=U.liter,
),
compartments=[
Compartment(
sid="bioreactor",
value=1.0,
unit=U.liter,
constant=True,
name="bioreactor",
spatialDimensions=3,
),
],
)
model.species = [
Species(
sid="Glcxt",
name="glucose",
initialConcentration=0.0,
substanceUnit=U.mmole,
hasOnlySubstanceUnits=False,
compartment="bioreactor",
),
Species(
sid="Ac",
name="acetate",
initialConcentration=0.0,
substanceUnit=U.mmole,
hasOnlySubstanceUnits=False,
compartment="bioreactor",
),
Species(
sid="O2",
name="oxygen",
initialConcentration=0.0,
substanceUnit=U.mmole,
hasOnlySubstanceUnits=False,
compartment="bioreactor",
),
Species(
sid="X",
name="biomass",
initialConcentration=0.0,
substanceUnit=U.mmole,
hasOnlySubstanceUnits=False,
compartment="bioreactor",
),
Species(
sid="s_Rv0649",
name="s_Rv0649 (GeneProduct)",
initialConcentration=0.0,
substanceUnit=U.mmole,
hasOnlySubstanceUnits=False,
compartment="bioreactor",
),
]
[docs]FLUX_BOUND_ZERO = "zero"
[docs]FLUX_BOUND_PLUS_INF = "ub_inf"
[docs]FLUX_BOUND_MINUS_INF = "lb_inf"
[docs]FLUX_BOUND_GLC_IMPORT = "glc_import"
[docs]FLUX_BOUND_O2_IMPORT = "o2_import"
model.parameters = [
# bounds
Parameter(
sid=FLUX_BOUND_ZERO,
name="zero bound",
value=0.0,
unit=U.mmole_per_hr,
constant=True,
sboTerm=SBO.FLUX_BOUND,
),
Parameter(
sid=FLUX_BOUND_PLUS_INF,
name="default upper bound",
value=float("Inf"),
unit=U.mmole_per_hr,
constant=True,
sboTerm=SBO.FLUX_BOUND,
),
Parameter(
sid=FLUX_BOUND_MINUS_INF,
name="default lower bound",
value=-float("Inf"),
unit=U.mmole_per_hr,
constant=True,
sboTerm=SBO.FLUX_BOUND,
),
Parameter(
sid=FLUX_BOUND_GLC_IMPORT,
name="glc import bound",
value=-15,
unit=U.mmole_per_hr,
constant=True,
sboTerm=SBO.FLUX_BOUND,
),
Parameter(
sid=FLUX_BOUND_O2_IMPORT,
name="o2 import bound",
value=-10,
unit=U.mmole_per_hr,
constant=True,
sboTerm=SBO.FLUX_BOUND,
),
]
model.gene_products = [
GeneProduct(
sid="gene1",
metaId="meta_gene_1",
label="Rv0649",
associatedSpecies="s_Rv0649",
annotations=[(BQB.IS, "kegg.genes/mtu:Rv0649")],
),
GeneProduct("g_b3670", label="b3670", name="b3670"),
GeneProduct("g_b3671", label="b3671", name="b3671"),
GeneProduct("g_b0077", label="b0077", name="b0077"),
GeneProduct("g_b0078", label="b0078", name="b0078"),
GeneProduct("g_b3768", label="b3768", name="b3768"),
GeneProduct("g_b3769", label="b3769", name="b3769"),
GeneProduct("g_b3767", label="b3767", name="b3767"),
]
model.reactions = [
Reaction(
sid="v1",
name="v1 (39.43 Ac + 35 O2 -> X)",
equation="39.43 Ac + 35 O2 => X []",
# geneProductAssociation="((g_b3670 and g_b3671) or (g_b0077 and g_b0078) or (g_b3768 and g_b3769 and g_b3767))"
geneProductAssociation="g_b3767",
),
Reaction(
sid="v2",
name="v2 (9.46 Glcxt + 12.92 O2 -> X)",
equation="9.46 Glcxt + 12.92 O2 => X []",
),
Reaction(
sid="v3",
name="v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X)",
equation="9.84 Glcxt + 12.73 O2 => 1.24 Ac + X []",
),
Reaction(
sid="v4",
name="v4 (19.23 Glcxt -> 12.12 Ac + X)",
equation="19.23 Glcxt => 12.12 Ac + X []",
),
]
for rt in model.reactions:
if rt.sid in ["v1", "v2", "v3", "v4"]:
rt.compartment = "bioreactor"
rt.lowerFluxBound = FLUX_BOUND_ZERO
rt.upperFluxBound = FLUX_BOUND_PLUS_INF
model.reactions.extend(
[
ExchangeReaction(
species_id="Ac",
lowerFluxBound=FLUX_BOUND_MINUS_INF,
upperFluxBound=FLUX_BOUND_PLUS_INF,
),
ExchangeReaction(
species_id="O2",
lowerFluxBound=FLUX_BOUND_O2_IMPORT,
upperFluxBound=FLUX_BOUND_ZERO,
),
ExchangeReaction(
species_id="Glcxt",
lowerFluxBound=FLUX_BOUND_GLC_IMPORT,
upperFluxBound=FLUX_BOUND_ZERO,
),
ExchangeReaction(
species_id="X",
lowerFluxBound=FLUX_BOUND_MINUS_INF,
upperFluxBound=FLUX_BOUND_PLUS_INF,
),
]
)
# -----------------------------------------------------------------------------
# Objective function
# -----------------------------------------------------------------------------
model.objectives = [
Objective(
sid="biomass_max",
objectiveType="maximize",
active=True,
fluxObjectives={"v1": 1.0, "v2": 1.0, "v3": 1.0, "v4": 1.0},
variableType="linear",
)
]
if __name__ == "__main__":
from sbmlutils.resources import EXAMPLES_DIR
create_model(model=model, filepath=EXAMPLES_DIR / f"{model.sid}.xml")