def create_assigment_rule(sbml_model: libsbml.Model,
assignee_id: str,
formula: str,
rule_id: str = None,
rule_name: str = None) -> libsbml.AssignmentRule:
"""Create SBML AssignmentRule
Arguments:
sbml_model: Model to add output to
assignee_id: Target of assignment
formula: Formula string for model output
rule_id: SBML id for created rule
rule_name: SBML name for created rule
Returns:
The created ``AssignmentRule``
"""
warn("This function will be removed in future releases.",
DeprecationWarning)
if rule_id is None:
rule_id = assignee_id
if rule_name is None:
rule_name = rule_id
rule = sbml_model.createAssignmentRule()
rule.setId(rule_id)
rule.setName(rule_name)
rule.setVariable(assignee_id)
rule.setFormula(formula)
return rule
def create_assigment_rule(sbml_model: libsbml.Model,
assignee_id: str,
formula: str,
rule_id: str = None,
rule_name: str = None):
"""Create SBML AssignmentRule
Arguments:
sbml_model: Model to add output to
assignee_id: Target of assignment
formula: Formula string for model output
rule_id: SBML id for created rule
rule_name: SBML name for created rule
"""
if rule_id is None:
rule_id = assignee_id
if rule_name is None:
rule_name = rule_id
rule = sbml_model.createAssignmentRule()
rule.setId(rule_id)
rule.setName(rule_name)
rule.setVariable(assignee_id)
rule.setFormula(formula)
return rule
def add_interpolator_to_model(interpolator: "Interpolator",
model: libsbml.Model) -> None:
"""Add interpolator to model.
The parameters, formulas and rules have to be added to the SBML model.
:param interpolator:
:param model: Model
:return:
"""
# create parameter
pid = interpolator.yid
# if parameter exists remove it
if model.getParameter(pid):
logger.warning(
"Model contains parameter: {}. Parameter is removed.".format(
pid))
model.removeParameter(pid)
# if assignment rule exists remove it
for rule in model.getListOfRules():
if rule.isAssignment():
if rule.getVariable() == pid:
model.removeRule(rule)
break
p = model.createParameter()
p.setId(pid)
p.setName(pid)
p.setConstant(False)
# create rule
rule = model.createAssignmentRule()
rule.setVariable(pid)
formula = interpolator.formula()
ast_node = libsbml.parseL3FormulaWithModel(formula, model)
if ast_node is None:
logger.warning(libsbml.getLastParseL3Error())
else:
rule.setMath(ast_node)
def _create_time(model: sbml.Model, time_var: str):
"""
Creates the time variable, add assignment to 'time'
Arguments:
model: the SBML model to which the species will be added.
time_var: str, the time variable
Returns:
Raises:
"""
time_parameter = model.createParameter()
time_parameter.setId(time_var)
time_parameter.setName(time_var)
time_parameter.setConstant(False)
time_assignment = model.createAssignmentRule()
time_assignment.setVariable(time_var)
time_assignment.setMath(sbml.parseL3Formula('time'))
def _create_assignment(model: sbml.Model, assignment_id: str, formula: str):
"""
Creates an assignment rule, that assigns id to formula.
Arguments:
model: SBML model to which the assignment rule will be added.
assignment_id: str, the id of the assignment rule
formula: str: contains the equation for the assignment rule
Returns:
Raises:
"""
assignment_parameter = model.createParameter()
assignment_parameter.setId(assignment_id)
assignment_parameter.setName(assignment_id)
assignment_parameter.setConstant(False)
assignment_parameter.setUnits('dimensionless')
assignment_rule = model.createAssignmentRule()
assignment_rule.setVariable(assignment_id)
assignment_rule.setMath(sbml.parseL3Formula(formula))