sbmlmath¶

Conversion of CellML maths to libsbml ASTs.

The libcellml analyser gives every equation as a binary tree of AnalyserEquationAst nodes with the variables resolved. ast_to_sbml walks such a tree into a libsbml.ASTNode; the variable of integration becomes the SBML time symbol, variables get their SBML id. mathml_to_sbml reads the MathML of a reset with libsbml and remaps the ci names the same way.

The analyser AST has the values of the numbers but not their units. NumberUnits reads them from the MathML of the components and finds the equation of an analyser AST by its variables and numbers.

MathConversionError ¶

Bases: ValueError

A CellML expression cannot be converted to SBML.

NumberUnits ¶

NumberUnits(model, ids, unit_id)

Units of the numbers of the equations of a CellML model.

The equations are read from the MathML of the components. An analyser AST is matched with the equation which has the same variables and numbers in the same order; the analyser may have rearranged an equation, which is then found by its variables and numbers in any order and gives the units by the value of the numbers. An equation is handed out once, so equations which only differ in their units stay apart.

Read the numbers of all equations.

Parameters:

Name	Type	Description	Default
`model`	`Model`	the (flattened) CellML model.	required
`ids`	`VariableIds`	SBML ids of the model.	required
`unit_id`	`Callable[[str], str]`	SBML unit id of a CellML units name.	required

units_of ¶

units_of(ast)

Units of the numbers of an equation.

Parameters:

Name	Type	Description	Default
`ast`	`Any`	root of the analyser AST of the equation.	required

Returns:

Type	Description
`_Units`	The units of its numbers from the left to the right, for
`_Units`	`ast_to_sbml`; `None` when the AST has no numbers or the
`_Units`	equation is not found (logged).

variable_node ¶

variable_node(variable, ids)

AST node referencing a CellML variable.

Parameters:

Name	Type	Description	Default
`variable`	`Any`	libcellml variable.	required
`ids`	`VariableIds`	SBML ids of the model.	required

Returns:

Type	Description
`ASTNode`	The `time` symbol for the variable of integration, else the name node
`ASTNode`	with the SBML id.

count_numbers ¶

count_numbers(node)

Number of cn nodes of an analyser AST.

Parameters:

Name	Type	Description	Default
`node`	`Any`	`libcellml.AnalyserEquationAst`, may be `None`.	required

Returns:

Type	Description
`int`	How many units of `NumberUnits.units_of` belong to `node`.

ast_to_sbml ¶

ast_to_sbml(node, ids, units=None)

Convert an analyser AST into a libsbml AST.

Parameters:

Name	Type	Description	Default
`node`	`Any`	`libcellml.AnalyserEquationAst`, e.g. the right child of the `EQUALITY` root of an equation.	required
`ids`	`VariableIds`	SBML ids of the model.	required
`units`	`_Units`	SBML units of the numbers below `node`, from the left to the right (`NumberUnits.units_of`); a number takes the next one, no units when it is `None`.	`None`

Returns:

Type	Description
`ASTNode`	The libsbml AST.

Raises:

Type	Description
`MathConversionError`	for a node type without SBML counterpart, e.g. `DIFF` or `BVAR` outside the left side of an ODE.

mathml_to_sbml ¶

mathml_to_sbml(mathml, component_name, ids, unit_id=None)

Read CellML MathML with libsbml and remap the variable names.

Used for the maths of resets, which the analyser does not cover. Units on numbers (cellml:units) become sbml:units.

Parameters:

Name	Type	Description	Default
`mathml`	`str`	complete `math` element.	required
`component_name`	`str`	component the MathML belongs to, resolves the names.	required
`ids`	`VariableIds`	SBML ids of the model.	required
`unit_id`	`Callable[[str], str] \| None`	SBML unit id of a CellML units name, the name itself when `None`.	`None`

Returns:

Type	Description
`ASTNode`	The libsbml AST.

Raises:

Type	Description
`MathConversionError`	if the MathML does not parse or a name is unknown.