def create_port_doc():
sbmlns = libsbml.SBMLNamespaces(3, 1, "comp", 1)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
model = doc.createModel()
model.setId("toy_update")
model.setName("toy (UPDATE submodel)")
model.setSBOTerm(SBO_CONTINOUS_FRAMEWORK)
objects = [
fac.Compartment(
sid="extern",
value=1.0,
unit="m3",
constant=True,
name="external compartment",
),
fac.Species(
sid="A",
name="A",
initialConcentration=10.0,
hasOnlySubstanceUnits=True,
compartment="extern",
),
fac.Species(
sid="C",
name="C",
initialConcentration=0,
hasOnlySubstanceUnits=True,
compartment="extern",
),
fac.Parameter(sid="EX_A",
value=1.0,
constant=False,
sboTerm="SBO:0000613"),
fac.Parameter(sid="EX_C",
value=1.0,
constant=False,
sboTerm="SBO:0000613"),
]
fac.create_objects(model, obj_iter=objects)
return doc
def create_fba_doc():
sbmlns = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPackageNamespace("fbc", 2)
sbmlns.addPackageNamespace("comp", 1)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired("comp", True)
doc.setPackageRequired("fbc", False)
model = doc.createModel()
mplugin = model.getPlugin("fbc")
mplugin.setStrict(True)
objects = [
fac.Compartment(sid='cell', value=1.0),
fac.Species(sid='A', initialConcentration=0, compartment="cell"),
fac.Species(sid='B', initialConcentration=0, compartment="cell"),
]
fac.create_objects(model, objects)
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='cell',
value=1.0,
unit=UNIT_VOLUME,
constant=True,
name='cell',
spatialDimensions=3),
# exchange species
mc.Species(sid='atp',
name="ATP",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
compartment="cell"),
mc.Species(sid='adp',
name="ADP",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
compartment="cell"),
mc.Species(sid='glc',
name="Glucose",
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
compartment="cell"),
mc.Species(sid='pyr',
name='Pyruvate',
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
compartment="cell"),
# internal species
mc.Species(sid='fru16bp',
name='Fructose 1,6-bisphospate',
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
compartment="cell"),
mc.Species(sid='pg2',
name='2-Phosphoglycerate',
initialConcentration=0,
substanceUnit=UNIT_AMOUNT,
hasOnlySubstanceUnits=False,
compartment="cell"),
# bounds
mc.Parameter(sid="ub_R3",
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="glu + 2 atp -> fru16bp + 2 adp",
fast=False,
reversible=False,
reactants={
"glc": 1,
"atp": 2
},
products={
"fru16bp": 1,
'adp': 2
},
compartment='cell')
r2 = mc.create_reaction(model,
rid="R2",
name="fru16bp -> 2 pg2",
fast=False,
reversible=False,
reactants={"fru16bp": 1},
products={"pg2": 2},
compartment='cell')
r3 = mc.create_reaction(model,
rid="R3",
name="pg2 + adp -> pyr + atp",
fast=False,
reversible=False,
reactants={
"pg2": 1,
"adp": 2
},
products={
"pyr": 1,
"atp": 2
},
compartment='cell')
# flux bounds
fbc.set_flux_bounds(r1, lb="zero", ub="ub_default")
fbc.set_flux_bounds(r2, lb="zero", ub="ub_default")
fbc.set_flux_bounds(r3, lb="zero", ub="ub_R3")
# fbc.set_flux_bounds(ratp, lb="zero", ub="ub_RATP")
# exchange reactions
for sid in ['atp', 'adp', 'glc', 'pyr']:
builder.create_exchange_reaction(model,
species_id=sid,
flux_unit=UNIT_FLUX)
# objective function
model_fbc = model.getPlugin("fbc")
fbc.create_objective(model_fbc,
oid="RATP_maximize",
otype="maximize",
fluxObjectives={"R3": 1.0},
active=True)
if annotations:
annotator.annotate_sbml_doc(doc, annotations)
# write SBML
sbmlio.write_sbml(doc,
filepath=os.path.join(directory, sbml_file),
validate=True)
return doc
for unit in units:
ports.append(
mcomp.Port(sid="{}{}".format(unit.sid, PORT_SUFFIX), unitRef=unit.sid))
##############################################################
# Functions
##############################################################
functions = []
##############################################################
# Compartments
##############################################################
compartments = [
mc.Compartment('Vpl',
value=3.0,
unit=UNIT_KIND_LITRE,
constant=False,
name='plasma',
port=True),
mc.Compartment('Vrbc',
value=0.0,
unit=UNIT_KIND_LITRE,
constant=False,
name='erythrocyte'),
]
##############################################################
# Species
##############################################################
# tissue metabolites
species = [
for unit in units:
ports.append(
mcomp.Port(sid="{}{}".format(unit.sid, PORT_SUFFIX), unitRef=unit.sid)
)
##############################################################
# Functions
##############################################################
functions = []
##############################################################
# Compartments
##############################################################
compartments = [
mc.Compartment('Vli', value=1.47, unit=UNIT_KIND_LITRE, constant=False, name='liver', port=True),
mc.Compartment('Vext', value=1.0, unit=UNIT_KIND_LITRE, constant=False, name='liver blood', port=True),
]
##############################################################
# Species
##############################################################
species = [
mc.Species('Aext_glc', compartment="Vext", initialConcentration=5.0, unit='mmole',
name="glucose", hasOnlySubstanceUnits=True, port=True),
mc.Species('Aext_lac', compartment="Vext", initialConcentration=0.8, unit='mmole',
name="lactate", hasOnlySubstanceUnits=True, port=True),
mc.Species('Ali_glc', compartment="Vli", initialConcentration=5.0, unit='mmole',
name="glucose", hasOnlySubstanceUnits=True),
mc.Species('Ali_lac', compartment="Vli", initialConcentration=0.8, unit='mmole',
name="lactate", hasOnlySubstanceUnits=True),
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
])
##############################################################
# Functions
##############################################################
functions.extend([
mc.Function('max', 'lambda(x,y, piecewise(x,gt(x,y),y) )', name='minimum of arguments'),
mc.Function('min', 'lambda(x,y, piecewise(x,lt(x,y),y) )', name='maximum of arguments'),
])
##############################################################
# Compartments
##############################################################
compartments.extend([
mc.Compartment(sid='ext', unit=UNIT_KIND_LITRE, constant=False, value=1.0, name='blood', port=True),
mc.Compartment(sid='cyto', unit=UNIT_KIND_LITRE, constant=False, value='V_cyto', name='cytosol', port=True),
mc.Compartment(sid='mito', unit=UNIT_KIND_LITRE, constant=False, value='V_mito', name='mitochondrion'),
mc.Compartment(sid='pm', spatialDimensions=2, unit='m2', constant=True, value='1.0 m2', name='plasma membrane'),
mc.Compartment(sid='mm', spatialDimensions=2, unit='m2', constant=True, value='1.0 m2',
name='mitochondrial membrane'),
])
##############################################################
# Species
##############################################################
species.extend([
mc.Species('Aatp', compartment='cyto', initialConcentration=2.8000, unit='mmole', boundaryCondition=True, hasOnlySubstanceUnits=True, name='ATP'),
mc.Species('Aadp', compartment='cyto', initialConcentration=0.8000, unit='mmole', boundaryCondition=True, hasOnlySubstanceUnits=True, name='ADP'),
mc.Species('Aamp', compartment='cyto', initialConcentration=0.1600, unit='mmole', boundaryCondition=True, hasOnlySubstanceUnits=True, name='AMP'),
mc.Species('Autp', compartment='cyto', initialConcentration=0.2700, unit='mmole', boundaryCondition=False, hasOnlySubstanceUnits=True, name='UTP'),
def test_modelcreator_notebook():
"""
If this test fails the respective notebook must be updated:
:return:
"""
import libsbml
from libsbml import (UNIT_KIND_SECOND, UNIT_KIND_ITEM, UNIT_KIND_MOLE,
UNIT_KIND_KILOGRAM, UNIT_KIND_METRE, UNIT_KIND_LITRE)
from sbmlutils import comp
from sbmlutils import fbc
from sbmlutils import sbmlio
from sbmlutils import factory as fac
from sbmlutils.dfba import builder, utils
main_units = {
'time': 's',
'extent': UNIT_KIND_ITEM,
'substance': UNIT_KIND_ITEM,
'length': 'm',
'area': 'm2',
'volume': 'm3',
}
units = [
fac.Unit('s', [(UNIT_KIND_SECOND, 1.0)]),
fac.Unit('item', [(UNIT_KIND_ITEM, 1.0)]),
fac.Unit('kg', [(UNIT_KIND_KILOGRAM, 1.0)]),
fac.Unit('m', [(UNIT_KIND_METRE, 1.0)]),
fac.Unit('m2', [(UNIT_KIND_METRE, 2.0)]),
fac.Unit('m3', [(UNIT_KIND_METRE, 3.0)]),
fac.Unit('mM', [(UNIT_KIND_MOLE, 1.0, 0),
(UNIT_KIND_METRE, -3.0)]),
fac.Unit('per_s', [(UNIT_KIND_SECOND, -1.0)]),
fac.Unit('item_per_s', [(UNIT_KIND_ITEM, 1.0),
(UNIT_KIND_SECOND, -1.0)]),
fac.Unit('item_per_m3', [(UNIT_KIND_ITEM, 1.0),
(UNIT_KIND_METRE, -3.0)]),
]
UNIT_TIME = 's'
UNIT_AMOUNT = 'item'
UNIT_AREA = 'm2'
UNIT_VOLUME = 'm3'
UNIT_CONCENTRATION = 'item_per_m3'
UNIT_FLUX = 'item_per_s'
# Create SBMLDocument with fba
doc = builder.template_doc_fba(model_id="toy")
model = doc.getModel()
utils.set_units(model, units)
utils.set_main_units(model, main_units)
objects = [
# compartments
fac.Compartment(sid='extern', value=1.0, unit=UNIT_VOLUME, constant=True, name='external compartment',
spatialDimensions=3),
fac.Compartment(sid='cell', value=1.0, unit=UNIT_VOLUME, constant=True, name='cell', spatialDimensions=3),
fac.Compartment(sid='membrane', value=1.0, unit=UNIT_AREA, constant=True, name='membrane', spatialDimensions=2),
# exchange species
fac.Species(sid='A', name="A", value=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
fac.Species(sid='C', name="C", value=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
# internal species
fac.Species(sid='B1', name="B1", value=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="cell"),
fac.Species(sid='B2', name="B2", value=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="cell"),
# bounds
fac.Parameter(sid="ub_R1", value=1.0, unit=UNIT_FLUX, constant=True, sboTerm=builder.FLUX_BOUND_SBO),
fac.Parameter(sid="zero", value=0.0, unit=UNIT_FLUX, constant=True, sboTerm=builder.FLUX_BOUND_SBO),
fac.Parameter(sid="ub_default", value=builder.UPPER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True,
sboTerm=builder.FLUX_BOUND_SBO),
]
fac.create_objects(model, objects)
# reactions
r1 = fac.create_reaction(model, rid="R1", name="A import (R1)", fast=False, reversible=True,
reactants={"A": 1}, products={"B1": 1}, compartment='membrane')
r2 = fac.create_reaction(model, rid="R2", name="B1 <-> B2 (R2)", fast=False, reversible=True,
reactants={"B1": 1}, products={"B2": 1}, compartment='cell')
r3 = fac.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")
fac.create_objective(model_fbc, oid="R3_maximize", otype="maximize",
fluxObjectives={"R3": 1.0}, active=True)
# write SBML file
import tempfile
sbml_file = tempfile.NamedTemporaryFile(suffix=".xml")
sbmlio.write_sbml(doc=doc, filepath=sbml_file.name)
(UNIT_KIND_SECOND, -1.0, 0, 3600)]),
mc.Unit('min_per_h', [(UNIT_KIND_SECOND, 1.0, 0, 60),
(UNIT_KIND_SECOND, -1.0, 0, 3600)]),
mc.Unit('ml_per_litre', [(UNIT_KIND_LITRE, 1.0, -3, 1.0),
(UNIT_KIND_LITRE, -1.0, 0, 1)]),
mc.Unit('mulitre_per_g', [(UNIT_KIND_LITRE, 1.0, -6, 1.0),
(UNIT_KIND_GRAM, -1.0, 0, 1)]),
]
##############################################################
# Compartments
##############################################################
compartments = [
mc.Compartment('Vre',
value=1,
unit=UNIT_KIND_LITRE,
constant=False,
name='rest of body'),
mc.Compartment('Vgu',
value=1,
unit=UNIT_KIND_LITRE,
constant=False,
name='gut'),
mc.Compartment('Vki',
value=1,
unit=UNIT_KIND_LITRE,
constant=False,
name='kidney'),
mc.Compartment('Vli',
value=1,
unit=UNIT_KIND_LITRE,
for unit in units:
ports.append(
mcomp.Port(sid="{}{}".format(unit.sid, PORT_SUFFIX), unitRef=unit.sid))
##############################################################
# Functions
##############################################################
functions = []
##############################################################
# Compartments
##############################################################
compartments = [
mc.Compartment('Vbr',
value=1.4,
unit=UNIT_KIND_LITRE,
constant=False,
name='brain tissue',
port=True),
mc.Compartment('Vext',
value=1.0,
unit=UNIT_KIND_LITRE,
constant=False,
name='brain blood',
port=True),
]
##############################################################
# Species
##############################################################
species = [
mc.Species('Aext_glc',
