amici.pysb_import

PySB Import

This module provides all necessary functionality to import a model specified in the pysb.core.Model format.

Functions Summary

extract_monomers(complex_patterns)	Constructs a list of monomer names contained in complex patterns.
has_fixed_parameter_ic(specie, pysb_model, …)	Wrapper to interface ode_export.ODEModel.state_has_fixed_parameter_initial_condition() from a pysb specie/model arguments
ode_model_from_pysb_importer(model[, …])	Creates an amici.ODEModel instance from a pysb.Model instance.
pysb2amici(model[, output_dir, observables, …])	Generate AMICI C++ files for the model provided to the constructor.
pysb_model_from_path(pysb_model_file)	Load a pysb model module and return the pysb.Model instance

Functions

amici.pysb_import.extract_monomers(complex_patterns)

Constructs a list of monomer names contained in complex patterns. Multiplicity of names corresponds to the stoichiometry in the complex.

Parameters

complex_patterns (typing.Union[pysb.core.ComplexPattern, typing.List[pysb.core.ComplexPattern]]) – (list of) complex pattern(s)

Return type

typing.List[str]

Returns

list of monomer names

amici.pysb_import.has_fixed_parameter_ic(specie, pysb_model, ode_model)

Wrapper to interface ode_export.ODEModel.state_has_fixed_parameter_initial_condition() from a pysb specie/model arguments

Parameters

• specie (pysb.core.ComplexPattern) – pysb species

• pysb_model (pysb.core.Model) – pysb model

• ode_model (amici.ode_export.ODEModel) – ODE model

Return type

bool

Returns

False if the species does not have an initial condition at all. Otherwise the return value of ode_export.ODEModel.state_has_fixed_parameter_initial_condition()

amici.pysb_import.ode_model_from_pysb_importer(model, constant_parameters=None, observables=None, sigmas=None, compute_conservation_laws=True, simplify=<function powsimp>, verbose=False)

Creates an amici.ODEModel instance from a pysb.Model instance.

Parameters

• model (pysb.core.Model) – see amici.pysb_import.pysb2amici()

• constant_parameters (typing.Optional[typing.List[str]]) – see amici.pysb_import.pysb2amici()

• observables (typing.Optional[typing.List[str]]) – see amici.pysb_import.pysb2amici()

• sigmas (typing.Optional[typing.Dict[str, str]]) – dict with names of observable Expressions as keys and names of sigma Expressions as value sigma

• compute_conservation_laws (bool) – see amici.pysb_import.pysb2amici()

• simplify (typing.Callable) – see amici.ODEModel._simplify

• verbose (typing.Union[int, bool]) – verbosity level for logging, True/False default to logging.DEBUG/logging.ERROR

Return type

amici.ode_export.ODEModel

Returns

New ODEModel instance according to pysbModel

amici.pysb_import.pysb2amici(model, output_dir=None, observables=None, constant_parameters=None, sigmas=None, verbose=False, assume_pow_positivity=False, compiler=None, compute_conservation_laws=True, compile=True, simplify=<function <lambda>>)

Generate AMICI C++ files for the model provided to the constructor.

Parameters

• model (pysb.core.Model) – pysb model, pysb.Model.name will determine the name of the generated module

• output_dir (typing.Optional[str]) – see amici.ode_export.ODEExporter.set_paths()

• observables (typing.Optional[typing.List[str]]) – list of pysb.core.Expression or pysb.core.Observable names in the provided model that should be mapped to observables

• sigmas (typing.Optional[typing.Dict[str, str]]) – dict of pysb.core.Expression names that should be mapped to sigmas

• constant_parameters (typing.Optional[typing.List[str]]) – list of pysb.core.Parameter names that should be mapped as fixed parameters

• verbose (typing.Union[int, bool]) – verbosity level for logging, True/False default to logging.DEBUG/logging.ERROR

• assume_pow_positivity (bool) – if set to true, a special pow function is used to avoid problems with state variables that may become negative due to numerical errors

• compiler (typing.Optional[str]) – distutils/setuptools compiler selection to build the python extension

• compute_conservation_laws (bool) – if set to true, conservation laws are automatically computed and applied such that the state-jacobian of the ODE right-hand-side has full rank. This option should be set to true when using the Newton algorithm to compute steadystates

• compile (bool) – If true, build the python module for the generated model. If false, just generate the source code.

• simplify (typing.Callable) – see amici.ODEModel._simplify

amici.pysb_import.pysb_model_from_path(pysb_model_file)

Load a pysb model module and return the pysb.Model instance

Parameters

pysb_model_file (str) – Full or relative path to the PySB model module

Return type

pysb.core.Model

Returns

The pysb Model instance