def save_sbml_model(model, filename, flavor=None):
""" Save a model to an SBML file.
Arguments:
model (Model): model
filename (str): file path
flavor (str): adapt to different modeling conventions (optional, currently available: 'cobra', 'fbc2')
"""
document = SBMLDocument(DEFAULT_SBML_LEVEL, DEFAULT_SBML_VERSION)
sbml_model = document.createModel(model.id)
if flavor in {Flavor.BIGG, Flavor.FBC2}:
document.enablePackage(FbcExtension.getXmlnsL3V1V2(), 'fbc', True)
fbc_model = sbml_model.getPlugin('fbc')
fbc_model.setStrict(True)
document.setPackageRequired('fbc', False)
_save_compartments(model, sbml_model)
_save_metabolites(model, sbml_model, flavor)
_save_reactions(model, sbml_model)
if isinstance(model, CBModel):
_save_cb_parameters(model, sbml_model, flavor)
_save_gpr_associations(model, sbml_model, flavor)
if isinstance(model, ODEModel):
_save_concentrations(model, sbml_model)
_save_global_parameters(model, sbml_model)
_save_kineticlaws(model, sbml_model)
_save_assignment_rules(model, sbml_model)
_save_metadata(model, sbml_model)
writer = SBMLWriter()
writer.writeSBML(document, filename)
def save_sbml_model(model, filename, flavor=None):
""" Save a model to an SBML file.
Arguments:
model (Model): model
filename (str): file path
flavor (str): adapt to different modeling conventions (optional, currently available: 'cobra', 'fbc2')
"""
document = SBMLDocument(DEFAULT_SBML_LEVEL, DEFAULT_SBML_VERSION)
sbml_model = document.createModel(model.id)
if flavor in {Flavor.BIGG, Flavor.FBC2}:
document.enablePackage(FbcExtension.getXmlnsL3V1V2(), 'fbc', True)
fbc_model = sbml_model.getPlugin('fbc')
fbc_model.setStrict(True)
document.setPackageRequired('fbc', False)
_save_compartments(model, sbml_model)
_save_metabolites(model, sbml_model, flavor)
_save_reactions(model, sbml_model)
if isinstance(model, CBModel):
_save_cb_parameters(model, sbml_model, flavor)
_save_gpr_associations(model, sbml_model, flavor)
if isinstance(model, ODEModel):
_save_concentrations(model, sbml_model)
_save_global_parameters(model, sbml_model)
_save_kineticlaws(model, sbml_model)
_save_assignment_rules(model, sbml_model)
_save_metadata(model, sbml_model)
writer = SBMLWriter()
writer.writeSBML(document, filename)
def flatten_external_model_definitions(
doc: libsbml.SBMLDocument,
validate: bool = False) -> libsbml.SBMLDocument:
"""Converts all ExternalModelDefinitions to ModelDefinitions.
I.e. the definition of models in external files are read
and directly included in the top model. The resulting
comp model consists than only of a single file.
The model refs in the submodel do not change in the process,
so no need to update the submodels.
:param doc: SBMLDocument
:param validate: validation flag
:return: SBMLDocument with ExternalModelDefinitions replaced
"""
logger.debug("* flattenExternalModelDefinitions")
# FIXME: handle multiple levels of hierarchies. Recursively to handle the ExternalModelDefinitions of submodels
logger.warning(
"flattenExternalModelDefinitions is experimental and does not work recursively!"
)
comp_doc = doc.getPlugin("comp")
if comp_doc is None:
logger.warning(
"Model is not a comp model, no ExternalModelDefinitions")
return doc
emd_list = comp_doc.getListOfExternalModelDefinitions()
if (emd_list is None) or (len(emd_list) == 0):
# no ExternalModelDefinitions
logger.warning("Model does not contain any ExternalModelDefinitions")
return doc
else:
emd_ids = []
for emd in emd_list:
logger.debug(emd)
emd_ids.append(emd.getId())
# get the model definition from the model
ref_model = emd.getReferencedModel()
ref_doc = ref_model.getSBMLDocument()
# print(ref_model)
for k in range(ref_doc.getNumPlugins()):
plugin = ref_doc.getPlugin(k)
# print(k, plugin)
# enable the package on the main SBMLDocument
uri = plugin.getURI()
prefix = plugin.getPrefix()
doc.enablePackage(uri, prefix, True)
# print("\n")
# add model definition for model
md = libsbml.ModelDefinition(ref_model)
comp_doc.addModelDefinition(md)
# remove the emds afterwards
for emd_id in emd_ids:
# remove the emd from the model
comp_doc.removeExternalModelDefinition(emd_id)
# validate
if validate:
validate_doc(doc)
return doc