petab.v1.sbml
Functions for interacting with SBML models
Functions
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Create an SBML model for the given condition. |
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Return SBML model parameters which are not Rule targets |
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Get an SBML model from file or URL or file handle |
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Turn all local parameters into global parameters with the same properties |
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Check for SBML validity / consistency |
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Load SBML model from file |
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Load SBML model from string |
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Log libsbml errors |
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Write PEtab visualization table |
- petab.v1.sbml.get_model_for_condition(petab_problem: Problem, sim_condition_id: str | None = None, preeq_condition_id: str | None = None) tuple[SBMLDocument, Model] [source]
Create an SBML model for the given condition.
Creates a copy of the model and updates parameters according to the PEtab files. Estimated parameters are set to their
nominalValue
. Observables defined in the observables table are not added to the model.- Parameters:
petab_problem – PEtab problem
sim_condition_id – Simulation
conditionId
for which to generate a modelpreeq_condition_id – Preequilibration
conditionId
of the settings for which to generate a model. This is only used to determine the relevant output parameter overrides. Preequilibration is not encoded in the resulting model.
- Returns:
The generated SBML document, and SBML model
- petab.v1.sbml.get_model_parameters(sbml_model: Model, with_values=False) list[str] | dict[str, float] [source]
Return SBML model parameters which are not Rule targets
- Parameters:
sbml_model – SBML model
with_values – If
False
, returns list of SBML model parameter IDs which are not Rule targets. IfTrue
, returns a dictionary with those parameter IDs as keys and parameter values from the SBML model as values.
- petab.v1.sbml.get_sbml_model(filepath_or_buffer) tuple[SBMLReader, SBMLDocument, Model] [source]
Get an SBML model from file or URL or file handle
- Parameters:
filepath_or_buffer – File or URL or file handle to read the model from
- Returns:
The SBML document, model and reader
- petab.v1.sbml.globalize_parameters(sbml_model: Model, prepend_reaction_id: bool = False) None [source]
Turn all local parameters into global parameters with the same properties
Local parameters are currently ignored by other PEtab functions. Use this function to convert them to global parameters. There may exist local parameters with identical IDs within different kinetic laws. This is not checked here. If in doubt that local parameter IDs are unique, enable
prepend_reaction_id
to create global parameters named${reaction_id}_${local_parameter_id}
.- Parameters:
sbml_model – The SBML model to operate on
prepend_reaction_id – Prepend reaction id of local parameter when creating global parameters
- petab.v1.sbml.is_sbml_consistent(sbml_document: SBMLDocument, check_units: bool = False) bool [source]
Check for SBML validity / consistency
- Parameters:
sbml_document – SBML document to check
check_units – Also check for unit-related issues
- Returns:
False
if problems were detected, otherwiseTrue
- petab.v1.sbml.load_sbml_from_file(sbml_file: str) tuple[SBMLReader, SBMLDocument, Model] [source]
Load SBML model from file
- Parameters:
sbml_file – Filename of the SBML file
- Returns:
The SBML reader, document, model
- petab.v1.sbml.load_sbml_from_string(sbml_string: str) tuple[SBMLReader, SBMLDocument, Model] [source]
Load SBML model from string
- Parameters:
sbml_string – Model as XML string
- Returns:
The SBML document, model and reader