amici.sbml_utils

SBML Utilities

This module provides helper functions for working with SBML.

Functions

`add_assignment_rule`(model, variable_id, formula)	Helper for adding an assignment rule to a SBML model.
`add_compartment`(model, compartment_id, *[, size])	Helper for adding a compartment to a SBML model.
`add_inflow`(model, species_id, rate, *[, ...])	rtype `libsbml.Reaction`
`add_parameter`(model, parameter_id, *[, ...])	Helper for adding a parameter to a SBML model.
`add_rate_rule`(model, variable_id, formula[, ...])	Helper for adding a rate rule to a SBML model.
`add_species`(model, species_id, *[, ...])	Helper for adding a species to a SBML model.
`create_sbml_model`(model_id[, level, version])	Helper for creating an empty SBML model.
`get_sbml_units`(model, x)	Try to get the units for expression x.
`mathml2sympy`(mathml, *[, evaluate, locals, ...])	rtype `sympy.core.basic.Basic`
`pretty_xml`(ugly_xml)	Prettifies an XML document (given as a string).
`sbml_math_ast`(expr, **kwargs)	Convert a SymPy expression to SBML math AST.
`sbml_mathml`(expr, *[, replace_time, pretty])	Prints a SymPy expression to a MathML expression parsable by libSBML.
`set_sbml_math`(obj, expr, **kwargs)	Set the math attribute of a SBML node using a SymPy expression.

Classes

MathMLSbmlPrinter([settings])

Prints a SymPy expression to a MathML expression parsable by libSBML.

Exceptions

`SbmlAnnotationError`
`SbmlDuplicateComponentIdError`
`SbmlInvalidIdSyntax`
`SbmlMathError`
`SbmlMissingComponentIdError`

class amici.sbml_utils.MathMLSbmlPrinter(settings=None)[source]

Prints a SymPy expression to a MathML expression parsable by libSBML.

Differences from sympy.MathMLContentPrinter: 1. underscores in symbol names are not converted to subscripts 2. symbols with name ‘time’ are converted to the SBML time symbol

__init__(settings=None)

apply_patch()

doprint(expr, *, pretty=False)[source]

Prints the expression as MathML.

Return type: str

emptyPrinter(expr)

mathml_tag(e): Returns the MathML tag for an expression.

property order

printmethod: str = '_mathml_content'

restore_patch()

classmethod set_global_settings(**settings): Set system-wide printing settings.

exception amici.sbml_utils.SbmlAnnotationError[source]

__init__(*args, **kwargs)

args

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception amici.sbml_utils.SbmlDuplicateComponentIdError[source]

__init__(*args, **kwargs)

args

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception amici.sbml_utils.SbmlInvalidIdSyntax[source]

__init__(*args, **kwargs)

args

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception amici.sbml_utils.SbmlMathError[source]

__init__(*args, **kwargs)

args

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception amici.sbml_utils.SbmlMissingComponentIdError[source]

__init__(*args, **kwargs)

args

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

amici.sbml_utils.add_assignment_rule(model, variable_id, formula, rule_id=None)[source]

Helper for adding an assignment rule to a SBML model.

Parameters

model (libsbml.Model) – SBML model to which the assignment rule is to be added.
variable_id (typing.Union[str, sympy.core.symbol.Symbol]) – SBML ID of the quantity for which the assignment rule is to be added.
formula – Formula for the assignment rule (it will be sympified).
rule_id (typing.Optional[str]) – SBML ID of the new assignment rule. Defaults to ‘assignment_’ + variableId.

Return type

libsbml.AssignmentRule

Returns

The assignment rule as a libsbml.AssignmentRule object.

amici.sbml_utils.add_compartment(model, compartment_id, *, size=1.0)[source]

Helper for adding a compartment to a SBML model.

Parameters

model (libsbml.Model) – SBML model to which the compartment is to be added.
compartment_id (typing.Union[str, sympy.core.symbol.Symbol]) – SBML ID of the new compartment.
size (float) – Size of the new compartment. Defaults to 1.0.

Return type

libsbml.Species

Returns

The new compartment as a libsbml.Compartment object.

amici.sbml_utils.add_inflow(model, species_id, rate, *, reaction_id=None, reversible=False)[source]

Return type: libsbml.Reaction

amici.sbml_utils.add_parameter(model, parameter_id, *, name=False, value=None, units=None, constant=None)[source]

Helper for adding a parameter to a SBML model.

Parameters

model (libsbml.Model) – SBML model to which the parameter is to be added.
parameter_id (typing.Union[str, sympy.core.symbol.Symbol]) – SBML ID of the new parameter.
name (typing.Union[bool, str]) – SBML name of the new parameter.
value (typing.Optional[float]) – Value attribute for the new parameter.
units (typing.Optional[str]) – Units attribute for the new parameter.
constant (typing.Optional[bool]) – Constant attribute for the new parameter.

Return type

libsbml.Parameter

Returns

The new parameter as a libsbml.Parameter object.

amici.sbml_utils.add_rate_rule(model, variable_id, formula, rule_id=None)[source]

Helper for adding a rate rule to a SBML model.

Parameters

model (libsbml.Model) – SBML model to which the rate rule is to be added.
variable_id (typing.Union[str, sympy.core.symbol.Symbol]) – SBML ID of the quantity for which the rate rule is to be added.
formula – Formula for the rate rule (it will be sympified).
rule_id (typing.Optional[str]) – SBML ID of the new rate rule. Defaults to ‘rate_’ + variableId.

Return type

libsbml.RateRule

Returns

The new rate rule as a libsbml.RateRule object.

amici.sbml_utils.add_species(model, species_id, *, compartment_id=None, name=False, initial_amount=0.0, units=None)[source]

Helper for adding a species to a SBML model.

Parameters

model (libsbml.Model) – SBML model to which the species is to be added.
species_id (typing.Union[str, sympy.core.symbol.Symbol]) – SBML ID of the new species.
compartment_id (typing.Optional[str]) – Compartment ID for the new species. If there is only one compartment it can be auto-selected.
initial_amount (float) – Initial amount of the new species.
units (typing.Optional[str]) – Units attribute for the new species.

Return type

libsbml.Species

Returns

The new species as a libsbml.Species object.

amici.sbml_utils.create_sbml_model(model_id, level=2, version=5)[source]

Helper for creating an empty SBML model.

Parameters

model_id (str) – SBML ID of the new model.
level (int) – Level of the new SBML document.
version (int) – Version of the new SBML document.

Return type

typing.Tuple[libsbml.SBMLDocument, libsbml.Model]

Returns

A tuple containing the newly created libsbml.SBMLDocument and libsbml.Model.

amici.sbml_utils.get_sbml_units(model, x)[source]

Try to get the units for expression x.

Parameters

model (libsbml.Model) – SBML model.
x (typing.Union[str, sympy.core.symbol.Symbol, sympy.core.basic.Basic]) – Expression to get the units of.

Return type

typing.Optional[str]

Returns

A string if the units could be determined, otherwise None.

amici.sbml_utils.mathml2sympy(mathml, *, evaluate=False, locals=None, expression_type='mathml2sympy')[source]

Return type: sympy.core.basic.Basic

amici.sbml_utils.pretty_xml(ugly_xml)[source]

Prettifies an XML document (given as a string).

Return type: str

amici.sbml_utils.sbml_math_ast(expr, **kwargs)[source]

Convert a SymPy expression to SBML math AST.

Parameters

expr – expression to be converted (will be sympified).
kwargs – extra options for MathML conversion.

Return type

libsbml.ASTNode

amici.sbml_utils.sbml_mathml(expr, *, replace_time=False, pretty=False, **settings)[source]

Prints a SymPy expression to a MathML expression parsable by libSBML.

Parameters

expr – expression to be converted to MathML (will be sympified).
replace_time (bool) – replace the AMICI time symbol with the SBML time symbol.
pretty (bool) – prettify the resulting MathML.

Return type

str

amici.sbml_utils.set_sbml_math(obj, expr, **kwargs)[source]

Set the math attribute of a SBML node using a SymPy expression.

Parameters

obj (libsbml.SBase) – SBML node supporting setMath method.
expr – expression to which the math attribute of obj should be se to (will be sympified).
kwargs – extra options for MathML conversion.

Return type

None