amici.ode_export

C++ Export

This module provides all necessary functionality specify an ODE model and generate executable C++ simulation code. The user generally won’t have to directly call any function from this module as this will be done by amici.pysb_import.pysb2amici(), amici.sbml_import.SbmlImporter.sbml2amici() and amici.petab_import.import_model().

Classes

`ConservationLaw`(identifier, name, value)	A conservation law defines the absolute the total amount of a (weighted) sum of states
`Constant`(identifier, name, value)	A Constant is a fixed variable in the model with respect to which sensitivities cannot be computed, abbreviated by `k`.
`Event`(identifier, name, value, state_update, ...)	An Event defines either a SBML event or a root of the argument of a Heaviside function.
`Expression`(identifier, name, value)	An Expression is a recurring elements in symbolic formulas.
`LogLikelihood`(identifier, name, value)	A LogLikelihood defines the distance between measurements and experiments for a particular observable.
`ModelQuantity`(identifier, name, value)	Base class for model components
`ODEExporter`(ode_model[, outdir, verbose, ...])	The ODEExporter class generates AMICI C++ files for ODE model as defined in symbolic expressions.
`ODEModel`([verbose, simplify])	Defines an Ordinary Differential Equation as set of ModelQuantities.
`Observable`(identifier, name, value[, ...])	An Observable links model simulations to experimental measurements, abbreviated by `y`.
`Parameter`(identifier, name, value)	A Parameter is a free variable in the model with respect to which sensitivities may be computed, abbreviated by `p`.
`SigmaY`(identifier, name, value)	A Standard Deviation SigmaY rescales the distance between simulations and measurements when computing residuals or objective functions, abbreviated by `sigmay`.
`State`(identifier, name, init, dt)	A State variable defines an entity that evolves with time according to the provided time derivative, abbreviated by `x`.
`TemplateAmici`(template)	Template format used in AMICI (see `string.Template` for more details).

Functions Summary

`apply_template`(source_file, target_file, ...)	Load source file, apply template substitution as provided in templateData and save as targetFile.
`cast_to_sym`(value, input_name)	Typecasts the value to `sympy.Float` if possible, and ensures the value is a symbolic expression.
`generate_flux_symbol`(reaction_index[, name])	Generate identifier symbol for a reaction flux.
`generate_measurement_symbol`(observable_id)	Generates the appropriate measurement symbol for the provided observable
`get_function_extern_declaration`(fun, name)	Constructs the extern function declaration for a given function
`get_model_override_implementation`(fun, name)	Constructs `amici::Model::*` override implementation for a given function
`get_sunindex_extern_declaration`(fun, name, ...)	Constructs the function declaration for an index function of a given function
`get_sunindex_override_implementation`(fun, ...)	Constructs the `amici::Model` function implementation for an index function of a given function
`is_valid_identifier`(x)	Check whether x is a valid identifier for conditions, parameters, observables.
`remove_typedefs`(signature)	Strips typedef info from a function signature
`smart_is_zero_matrix`(x)	A faster implementation of sympy's is_zero_matrix
`smart_jacobian`(eq, sym_var)	Wrapper around symbolic jacobian with some additional checks that reduce computation time for large matrices
`smart_multiply`(x, y)	Wrapper around symbolic multiplication with some additional checks that reduce computation time for large matrices
`strip_pysb`(symbol)	Strips pysb info from a `pysb.Component` object
`symbol_with_assumptions`(name)	Central function to create symbols with consistent, canonical assumptions
`var_in_function_signature`(name, varname)	Checks if the values for a symbolic variable is passed in the signature of a function

Functions

amici.ode_export.apply_template(source_file, target_file, template_data)[source]

Load source file, apply template substitution as provided in templateData and save as targetFile.

Parameters

source_file (str) – relative or absolute path to template file
target_file (str) – relative or absolute path to output file
template_data (typing.Dict[str, str]) – template keywords to substitute (key is template variable without TemplateAmici.delimiter)

Return type

None

amici.ode_export.cast_to_sym(value, input_name)[source]

Typecasts the value to sympy.Float if possible, and ensures the value is a symbolic expression.

Parameters

value (typing.Union[typing.SupportsFloat, sympy.core.expr.Expr, sympy.logic.boolalg.BooleanAtom]) – value to be cast
input_name (str) – name of input variable

Return type

sympy.core.expr.Expr

Returns

typecast value

amici.ode_export.generate_flux_symbol(reaction_index, name=None)[source]

Generate identifier symbol for a reaction flux. This function will always return the same unique python object for a given entity.

Parameters

reaction_index (int) – index of the reaction to which the flux corresponds
name (typing.Optional[str]) – an optional identifier of the reaction to which the flux corresponds

Return type

sympy.core.symbol.Symbol

Returns

identifier symbol

amici.ode_export.generate_measurement_symbol(observable_id)[source]

Generates the appropriate measurement symbol for the provided observable

Parameters: observable_id (typing.Union[str, sympy.core.symbol.Symbol]) – symbol (or string representation) of the observable
Returns: symbol for the corresponding measurement

amici.ode_export.get_function_extern_declaration(fun, name)[source]

Constructs the extern function declaration for a given function

Parameters

fun (str) – function name
name (str) – model name

Return type

str

Returns

C++ function definition string

amici.ode_export.get_model_override_implementation(fun, name, nobody=False)[source]

Constructs amici::Model::* override implementation for a given function

Parameters

fun (str) – function name
name (str) – model name
nobody (bool) – whether the function has a nontrivial implementation

Return type

str

Returns

C++ function implementation string

amici.ode_export.get_sunindex_extern_declaration(fun, name, indextype)[source]

Constructs the function declaration for an index function of a given function

Parameters

fun (str) – function name
name (str) – model name
indextype (str) – index function {‘colptrs’, ‘rowvals’}

Return type

str

Returns

C++ function declaration string

amici.ode_export.get_sunindex_override_implementation(fun, name, indextype, nobody=False)[source]

Constructs the amici::Model function implementation for an index function of a given function

Parameters

fun (str) – function name
name (str) – model name
indextype (str) – index function {‘colptrs’, ‘rowvals’}
nobody (bool) – whether the corresponding function has a nontrivial implementation

Return type

str

Returns

C++ function implementation string

amici.ode_export.is_valid_identifier(x)[source]

Check whether x is a valid identifier for conditions, parameters, observables… . Identifiers may only contain upper and lower case letters, digits and underscores, and must not start with a digit.

Parameters: x (str) – string to check
Return type: bool
Returns: True if valid, False otherwise

amici.ode_export.remove_typedefs(signature)[source]

Strips typedef info from a function signature

Parameters: signature (str) – function signature
Return type: str
Returns: string that can be used to construct function calls with the same variable names and ordering as in the function signature