def set_main_units(model, main_units):
""" Set main units information on model.
:param model: Model
:param main_units: units info
"""
factory.set_model_units(model, main_units)
def set_main_units(model, main_units):
""" Set main units information on model.
:param model: Model
:param main_units: units info
"""
factory.set_model_units(model, main_units)
def create_sbml(self, sbml_level=SBML_LEVEL, sbml_version=SBML_VERSION):
""" Create the SBML model
:return:
:rtype:
"""
from sbmlutils.validation import check
logging.info('*'*40)
logging.info(self.model_id)
logging.info('*' * 40)
# create core model
sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version)
# add all the packages
# FIXME: only add packages which are required for the model
sbmlns.addPackageNamespace("fbc", 2)
sbmlns.addPackageNamespace("comp", 1)
# sbmlns.addPackageNamespace("distrib", 1)
self.doc = libsbml.SBMLDocument(sbmlns)
self.doc.setPackageRequired("comp", True)
self.doc.setPackageRequired("fbc", False)
# self.doc.setPackageRequired("distrib", True)
self.model = self.doc.createModel()
fbc_plugin = self.model.getPlugin("fbc")
fbc_plugin.setStrict(False)
# name & id
check(self.model.setId(self.model_id), 'set id')
check(self.model.setName(self.model_id), 'set name')
# notes
if hasattr(self, 'notes') and self.notes is not None:
factory.set_notes(self.model, self.notes)
# history
if hasattr(self, 'creators'):
history.set_model_history(self.model, self.creators)
# model units
if hasattr(self, 'model_units'):
factory.set_model_units(self.model, self.model_units)
# lists ofs
for attr in [
'externalModelDefinitions',
'submodels',
'units',
'functions',
'parameters',
'compartments',
'species',
'assignments',
'rules',
'rate_rules',
'reactions',
'events',
'constraints',
'ports',
'replacedElements',
'deletions',
'objectives',
'layouts'
]:
# create the respective objects
if hasattr(self, attr):
objects = getattr(self, attr)
if objects:
factory.create_objects(self.model, obj_iter=objects, key=attr)
else:
logging.warning("Not defined: <{}> ".format(attr))
UNIT_CONCENTRATION = 'item_per_m3'
UNIT_FLUX = 'item_per_s'
# ### Model building
# Creation of FBA model using multiple packages (`comp`, `fbc`).
# In[3]:
# Create SBMLDocument with fba
doc = builder.template_doc_fba(model_id="toy")
model = doc.getModel()
factory.create_objects(model, units)
factory.set_model_units(model, model_units)
objects = [
# compartments
Compartment(sid='extern', value=1.0, unit=UNIT_VOLUME, constant=True, name='external compartment',
spatialDimensions=3),
Compartment(sid='cell', value=1.0, unit=UNIT_VOLUME, constant=True, name='cell', spatialDimensions=3),
Compartment(sid='membrane', value=1.0, unit=UNIT_AREA, constant=True, name='membrane', spatialDimensions=2),
# exchange species
Species(sid='A', name="A", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
Species(sid='C', name="C", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
# internal species
UNIT_CONCENTRATION = 'item_per_m3'
UNIT_FLUX = 'item_per_s'
# ### Model building
# Creation of FBA model using multiple packages (`comp`, `fbc`).
# In[3]:
# Create SBMLDocument with fba
doc = builder.template_doc_fba(model_id="toy")
model = doc.getModel()
factory.create_objects(model, units)
factory.set_model_units(model, model_units)
objects = [
# compartments
Compartment(sid='extern', value=1.0, unit=UNIT_VOLUME, constant=True, name='external compartment',
spatialDimensions=3),
Compartment(sid='cell', value=1.0, unit=UNIT_VOLUME, constant=True, name='cell', spatialDimensions=3),
Compartment(sid='membrane', value=1.0, unit=UNIT_AREA, constant=True, name='membrane', spatialDimensions=2),
# exchange species
Species(sid='A', name="A", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
Species(sid='C', name="C", initialAmount=0, substanceUnit=UNIT_AMOUNT, hasOnlySubstanceUnits=True,
compartment="extern"),
# internal species
def create_sbml(self, sbml_level=SBML_LEVEL, sbml_version=SBML_VERSION):
""" Create the SBML model
:return:
:rtype:
"""
from sbmlutils.validation import check
logging.info('*' * 40)
logging.info(self.model_id)
logging.info('*' * 40)
# create core model
sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version)
# add all the packages
# FIXME: only add packages which are required for the model
sbmlns.addPackageNamespace("fbc", 2)
sbmlns.addPackageNamespace("comp", 1)
# sbmlns.addPackageNamespace("distrib", 1)
self.doc = libsbml.SBMLDocument(sbmlns)
self.doc.setPackageRequired("comp", True)
self.doc.setPackageRequired("fbc", False)
# self.doc.setPackageRequired("distrib", True)
self.model = self.doc.createModel()
fbc_plugin = self.model.getPlugin("fbc")
fbc_plugin.setStrict(False)
# name & id
check(self.model.setId(self.model_id), 'set id')
check(self.model.setName(self.model_id), 'set name')
# notes
if hasattr(self, 'notes') and self.notes is not None:
factory.set_notes(self.model, self.notes)
# history
if hasattr(self, 'creators'):
history.set_model_history(self.model, self.creators)
# model units
if hasattr(self, 'model_units'):
factory.set_model_units(self.model, self.model_units)
# lists ofs
for attr in [
'externalModelDefinitions', 'submodels', 'units', 'functions',
'parameters', 'compartments', 'species', 'assignments',
'rules', 'rate_rules', 'reactions', 'events', 'constraints',
'ports', 'replacedElements', 'deletions', 'objectives',
'layouts'
]:
# create the respective objects
if hasattr(self, attr):
objects = getattr(self, attr)
if objects:
factory.create_objects(self.model,
obj_iter=objects,
key=attr)
else:
logging.info("Not defined: <{}> ".format(attr))
def create_sbml(
self, sbml_level: int = SBML_LEVEL, sbml_version: int = SBML_VERSION
) -> libsbml.SBMLDocument:
"""Create the SBML model
:return:
:rtype:
"""
logger.info(f"create_sbml: '{self.model_id}'")
# create core model
sbmlns = libsbml.SBMLNamespaces(sbml_level, sbml_version)
# add all the packages
# FIXME: only add packages which are required for the model
supported_packages = {"fbc", "comp", "distrib"}
sbmlns.addPackageNamespace("comp", 1)
for package in self.packages:
if package not in supported_packages:
raise ValueError(
f"Supported packages are: '{supported_packages}', "
f"but package '{package}' found."
)
if package == "fbc":
sbmlns.addPackageNamespace("fbc", 2)
if package == "distrib":
sbmlns.addPackageNamespace("distrib", 1)
self.doc = libsbml.SBMLDocument(sbmlns)
self.model = self.doc.createModel()
self.doc.setPackageRequired("comp", True)
if "fbc" in self.packages:
self.doc.setPackageRequired("fbc", False)
fbc_plugin = self.model.getPlugin("fbc")
fbc_plugin.setStrict(False)
if "distrib" in self.packages:
self.doc.setPackageRequired("distrib", True)
# name & id
if self.model_id:
check(self.model.setId(self.model_id), "set id")
check(self.model.setName(self.model_id), "set name")
else:
logger.warning("Model id 'mid' should be set on model")
# notes
if hasattr(self, "notes") and self.notes is not None:
factory.set_notes(self.model, self.notes)
# history
if hasattr(self, "creators"):
history.set_model_history(self.model, self.creators)
# model units
if hasattr(self, "model_units"):
factory.set_model_units(self.model, self.model_units)
# lists ofs
for attr in [
"externalModelDefinitions",
"submodels",
"units",
"functions",
"parameters",
"compartments",
"species",
"assignments",
"rules",
"rate_rules",
"reactions",
"events",
"constraints",
"ports",
"replacedElements",
"deletions",
"objectives",
"layouts",
]:
# create the respective objects
if hasattr(self, attr):
objects = getattr(self, attr)
if objects:
factory.create_objects(self.model, obj_iter=objects, key=attr)
else:
logger.debug(f"Not defined: <{attr}>")
return self.doc