petab.v2.models.pysb_model

Functions for handling PySB models

class petab.v2.models.pysb_model.PySBModel(model: Model, model_id: str | None = None)[source]

Bases: Model

PEtab wrapper for PySB models

static from_file(filepath_or_buffer, model_id: str | None = None)[source]

Load the model from the given path/URL

Parameters:
  • filepath_or_buffer – URL or path of the model

  • model_id – Model ID

Returns:

A Model instance holding the given model

get_free_parameter_ids_with_values() Iterable[tuple[str, float]][source]

Get free model parameters along with their values

Returns:

Iterator over tuples of (parameter_id, parameter_value)

get_parameter_ids() Iterable[str][source]

Get all parameter IDs from this model

Returns:

Iterator over model parameter IDs

get_parameter_value(id_: str) float[source]

Get a parameter value

Parameters:

id – ID of the parameter whose value is to be returned

Raises:

ValueError – If no parameter with the given ID exists

Returns:

The value of the given parameter as specified in the model

get_valid_ids_for_condition_table() Iterable[str][source]

Get IDs of all model entities that are allowed to occur as columns in the PEtab conditions table.

Returns:

Iterator over model entity IDs

get_valid_parameters_for_parameter_table() Iterable[str][source]

Get IDs of all parameters that are allowed to occur in the PEtab parameters table

Returns:

Iterator over parameter IDs

has_entity_with_id(entity_id) bool[source]

Check if there is a model entity with the given ID

Parameters:

entity_id – ID to check for

Returns:

True, if there is an entity with the given ID, False otherwise

is_state_variable(id_: str) bool[source]

Check whether the given ID corresponds to a model state variable

is_valid() bool[source]

Validate this model

Returns:

True if the model is valid, False if there are errors in this model

symbol_allowed_in_observable_formula(id_: str) bool[source]

Check if the given ID is allowed to be used in observable and noise formulas

Returns:

True, if allowed, False otherwise

to_file(filename: [<class 'str'>, <class 'pathlib.Path'>])[source]

Save the model to the given file

Parameters:

filename – Destination filename

petab.v2.models.pysb_model.parse_species_name(name: str) list[tuple[str, str | None, dict[str, Any]]][source]

Parse a PySB species name

Parameters:

name – Species name to parse

Returns:

List of species, representing complex constituents, each as a tuple of the monomer name, the compartment name, and a dict of sites mapping to site states.

Raises:

ValueError – In case this is not a valid ID

petab.v2.models.pysb_model.pattern_from_string(string: str, model: Model) ComplexPattern[source]

Convert a pattern string to a Pattern instance