sbmlmath¶

Functions

`sbml_math_to_sympy`(sbml_obj, **kwargs)	Convert SBML MathML to sympy expression.
`set_math`(element, expr)	Set the math expression of an SBML object.
`sympy_to_sbml_math`(sp_expr)	Convert sympy expression to SBML math ASTNode.

class sbmlmath.CFunction(*args, definition_url=None, encoding='text', **kwargs)[source]¶

Bases: UndefinedFunction

Represents <csymbol> functions.

Examples: rateOf(), delay(), distributions from the distrib package.

class sbmlmath.CSymbol(*args, definition_url, encoding='text', **kwargs)[source]¶

Bases: Dummy

Represents a <csymbol> element.

Represents, for example the Avogadro constant, which is defined in SBML as:

<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/avogadro"> avogadro </csymbol>

and can be generated by:

>>> CSymbol("avogadro", definition_url="http://www.sbml.org/sbml/symbols/avogadro")
<avogadro(http://www.sbml.org/sbml/symbols/avogadro)>
>>> float(CSymbol("avogadro", definition_url="http://www.sbml.org/sbml/symbols/avogadro"))
6.02214179e+23

Parameters:

definition_url (str)
encoding (str)

class sbmlmath.Delay(*args, **kwargs)[source]¶

Bases: CFunction

Produces a SBML delay() function.

Usually, it’s preferable to use the delay() function. This class can be used if a delay function with a different name is needed.

Examples

>>> from sympy.abc import a
>>> my_delay = Delay("my_delay")
>>> my_delay(a)
my_delay(a)
>>> delay(a) == my_delay(a)
True

class sbmlmath.RateOf(*args, **kwargs)[source]¶

Bases: CFunction

Produces a SBML rateOf() function.

Usually, it’s preferable to use the rate_of() function. This class can be used if a rateOf function with a different name is needed.

Examples

>>> from sympy.abc import a
>>> my_rate_of = RateOf("my_rate_of")
>>> my_rate_of(a)
my_rate_of(a)
>>> rate_of(a) == my_rate_of(a)
True
>>> rate_of(1)
0

class sbmlmath.SBMLMathMLParser(sbml_level=3, sbml_version=2, ureg=None, floats_as_rationals=True, ignore_units=False, symbol_kwargs=None, evaluate=False)[source]¶

Bases: object

MathML parser for sympy.

Parses the SBML subset of MathML 2.0.

For details, see SBML spec section 3.4: https://raw.githubusercontent.com/combine-org/combine-specifications/main/specifications/files/sbml.level-3.version-2.core.release-2.pdf.

See also: MathML 2.0 specification.

Parameters:

sbml_level (int | str) – SBML level. Note that SBML level < 3 has not been thoroughly tested.
sbml_version (int | str) – SBML version.
ureg (UnitRegistry) – Optional pint.UnitRegistry to use for unit conversion.
floats_as_rationals – Whether to convert floats to sympy.Rational. Improves precision.
ignore_units – Whether to ignore units. If True, all units are ignored and all numbers are converted to plain numbers. If False, all math elements with units are converted to pint.Quantity objects.
symbol_kwargs – Additional keyword arguments for constructing sympy.Symbol. For example, for passing custom assumptions such as real=True.

handle_apply(element)[source]¶

Handle <apply>

Return type:: Expr
Parameters:: element (_Element)

handle_ci(element)[source]¶

Handle identifiers.

Return type:: Expr
Parameters:: element (_Element)

handle_cn(element)[source]¶

Handle numbers.

Return type:: Expr
Parameters:: element (_Element)

parse_file(file_like)[source]¶

Parse a file-like object containing MathML.

Parameters:: file_like – File-like object (file, filename, …) containing MathML. Expected to contain the XML prolog <?xml [...]?> and the MathML math element.
Return type:: Expr
Returns:: The sympy representation of the MathML expression.

parse_str(mathml)[source]¶

Parse a string containing MathML.

Parameters:: mathml (str) – MathML string. Expected to contain the XML prolog <?xml [...]?> and the MathML math element.
Returns:: The sympy representation of the MathML expression.

preprocess_symbol_name(name, element=None)[source]¶

Preprocess symbol names.

Override this method to preprocess symbol names before parsing. For example, to handle reserved names.

Does nothing by default.

Parameters:

name (str) – Symbol name in the MathML element.
element (_Element) – MathML element.

Return type:

str

Returns:

Preprocessed symbol name.

class sbmlmath.SBMLMathMLPrinter(*args, literals_dimensionless=True, sbml_level=3, sbml_version=2, **kwargs)[source]¶

Bases: MathMLContentPrinter

MathML code printer.

This printer converts SymPy expressions to MathML code that can be used in SBML models.

Note:

assumes all constants are dimensionless

Parameters:

sbml_level (int)
sbml_version (int)

doprint(expr, with_prolog=True, with_math=True)[source]¶

Convert SymPy expression to MathML string.

Parameters:

expr – The SymPy expression to be converted.
with_prolog – Whether to include the XML prolog.
with_math – Whether to include the <math> tags.

Return type:

str

>>> SBMLMathMLPrinter().doprint(sp.sympify("3 * a"))
'<?xml version="1.0" encoding="UTF-8"?>\n<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:sbml="http://www.sbml.org/sbml/level3/version2/core">\n<apply><times/><cn type="integer" sbml:units="dimensionless">3</cn><ci>a</ci></apply></math>'

>>> SBMLMathMLPrinter().doprint(sp.sympify("cbrt(3)"), with_math=False, with_prolog=False)
'<apply><root/><degree><cn>3</cn></degree><cn type="integer" sbml:units="dimensionless">3</cn></apply>'

class sbmlmath.SpeciesSymbol(*args, representation_type=None, species_reference=None, **kwargs)[source]¶

Bases: Dummy

Represents a <ci> element containing a species.

Represents, for example, <ci multi:representationType="sum"> bla </ci> or <ci multi:speciesReference="refS"> S </ci> (see SBML multi specs 3.26).

Subclassed from sympy.Dummy to avoid caching issues, due to using the same name but with different attributes / meanings.

Parameters:

representation_type (Literal['sum', 'numericValue'] | None) – What the species symbol represents (see also SBML-multi spec 3.26.2).
species_reference (str) – ID of a species reference in the same reaction (see also SBML-multi spec 3.26.1).

>>> SpeciesSymbol("S") + SpeciesSymbol("S", representation_type="sum")
_S + _S

>>> SpeciesSymbol("S") == SpeciesSymbol("S", representation_type="sum")
False

>>> SpeciesSymbol("ref_to_S", species_reference="S")
<ref_to_S(species_reference=S)>

class sbmlmath.TimeSymbol(name)[source]¶

Bases: CSymbol

The current internal simulation time.

This symbol represents the current simulation time inside the model.

>>> TimeSymbol("t")
<t(http://www.sbml.org/sbml/symbols/time)>

Parameters:: name (str) – The name of the symbol.

class sbmlmath.delay(*args)¶: Bases: AppliedUndef

sbmlmath.rate_of¶: alias of rateOf

sbmlmath.sbml_math_to_sympy(sbml_obj, **kwargs)[source]¶

Convert SBML MathML to sympy expression.

Conversion is done using the default settings of SBMLMathMLParser.

Parameters:

sbml_obj (libsbml.SBase | libsbml.ASTNode) – The SBML object to be converted. (Either directly the ASTNode or the surrounding SBase object).
kwargs – Additional keyword arguments passed to SBMLMathMLParser.__init__.

Return type:

Expr

Returns:

The resulting sympy expression.

sbmlmath.set_math(element, expr)[source]¶

Set the math expression of an SBML object.

Parameters:

element (libsbml.SBase) – The SBML object to set the math expression for.
expr (Expr) – The sympy expression to set as the math expression.

Return type:

None

sbmlmath.sympy_to_sbml_math(sp_expr)[source]¶

Convert sympy expression to SBML math ASTNode.

This function takes a SymPy expression and converts it to an SBML math ASTNode.

Parameters:: sp_expr (Expr) – The SymPy expression to be converted.
Return type:: libsbml.ASTNode
Returns:: The resulting SBML math ASTNode.
Raises:: ValueError – If there is an error in converting the math expression.

Modules

`cfunction`	Handling of `<csymbol>` functions
`csymbol`	Handling of <csymbol> constants
`mathml_parser`	SBML mathml to sympy.
`mathml_printer`	Convenience functions for libsbml core
`species_symbol`	SBML MathML related functionality

sbmlmath¶

sbmlmath

Navigation

Related Topics