model.comparisons¶

The comparisons of the maths of an SBML model, which an engine shifts at their threshold.

The integrators of AMICI (CVODES) and of COPASI (LSODA) find the root of a comparison where its root function changes its sign, and not where it leaves 0: a comparison which is exactly at its threshold when the integrator starts to watch it is not found when it turns later. The models of both engines therefore compile a comparison shifted by a parameter, a > b + shift, which is 0 but at the start of an integration at which the comparison is exactly at its threshold, see shift_comparison.

trigger_comparisons ¶

trigger_comparisons(trigger, kinds=STRICT_COMPARISONS)

Get the comparisons of a trigger of given kinds, through its logical operators.

Parameters:

Name	Type	Description	Default
`trigger`	`ASTNode`	the math of the trigger.	required
`kinds`	`Sequence[int]`	the types of the nodes of the comparisons, the strict ones `>` and `<` by default (`STRICT_COMPARISONS`), or every comparison (`COMPARISONS`).	`STRICT_COMPARISONS`

Returns:

Type	Description
`list[_Found]`	The comparisons in the order of the math, each with its parent
`list[_Found]`	(`None` for the trigger itself) and its position in it.

math_comparisons ¶

math_comparisons(math, kinds)

Get the comparisons of given kinds anywhere in a math, e.g. in the conditions of its piecewises.

Parameters:

Name	Type	Description	Default
`math`	`ASTNode`	the math.	required
`kinds`	`Sequence[int]`	the types of the nodes of the comparisons.	required

Returns:

Type	Description
`list[_Found]`	The comparisons in the order of the math, a comparison before the
`list[_Found]`	ones in its operands, each with its parent (`None` for the math
`list[_Found]`	itself) and its position in it.

shift_comparison ¶

shift_comparison(comparison, pid)

Shift a comparison by a parameter so that it keeps its value at its threshold.

a > b becomes a > b + shift, a < b a + shift < b, a >= b a >= b - shift and a <= b a <= b + shift: a positive shift keeps the value of the comparison at its threshold until the operands move by the shift in the direction which changes it, a shift of 0 is the comparison as written.

Parameters:

Name	Type	Description	Default
`comparison`	`ASTNode`	the node of the comparison, changed in place.	required
`pid`	`str`	the id of the parameter of the shift.	required