def addEvent(
self,
trigger,
assignments,
persistent=True,
initial_value=False,
priority=0,
delay=0,
event_id="",
):
"""Add event supplied with when an event is triggered and
what happens using assignments in a dictionary.
"""
e1 = self.model.createEvent()
self.check(e1, "create event")
if len(event_id) == 0:
event_id = "e" + str(self.model.getNumEvents())
self.check(e1.setId(event_id), "add id to event")
if self.document.getLevel() == 3 or (self.document.getLevel() == 2 and
self.document.getVersion() == 4):
self.check(e1.setUseValuesFromTriggerTime(True),
"set use values from trigger time")
tri = e1.createTrigger()
self.check(tri, "add trigger to event")
tri_ast = libsbml.parseL3Formula(trigger)
self.check(tri.setMath(tri_ast), "add formula to trigger")
if self.document.getLevel() == 3:
self.check(tri.setPersistent(persistent),
"set persistence of trigger")
self.check(tri.setInitialValue(initial_value),
"set initial value of trigger")
de = e1.createDelay()
if self.document.getLevel() == 3:
k = self.addParameter(event_id + "Delay", delay,
self.model.getTimeUnits())
else:
k = self.addParameter(event_id + "Delay", delay, "time")
self.check(de, "add delay to event")
delay_ast = libsbml.parseL3Formula(k.getId())
self.check(de.setMath(delay_ast), "set formula for delay")
for a in assignments.keys():
assign = e1.createEventAssignment()
self.check(assign, "add event assignment to event")
self.check(assign.setVariable(a),
"add variable to event assignment")
val_ast = libsbml.parseL3Formula(assignments.get(a))
self.check(assign.setMath(val_ast),
"add value to event assignment")
if self.document.getLevel() == 3:
pri = e1.createPriority()
pri_ast = libsbml.parseL3Formula(str(priority))
self.check(pri.setMath(pri_ast), "add priority to event")
return e1
def addRateRule(self, var, math):
r = self.model.createRateRule()
self.check(r, 'create rate rule r')
self.check(r.setVariable(var), 'set rate rule variable')
math_ast = libsbml.parseL3Formula(math)
self.check(r.setMath(math_ast), 'set rate rule equation')
return r
def addRateRule(self, var, math):
r = self.model.createRateRule()
self.check(r, 'create rate rule r')
self.check(r.setVariable(var), 'set rate rule variable')
math_ast = libsbml.parseL3Formula(math)
self.check(r.setMath(math_ast), 'set rate rule equation')
return r
def addEvent(self, trigger, assignments, persistent=True, \
initial_value=False, priority=0, delay=0, event_id=''):
e1 = self.model.createEvent()
self.check(e1, 'create event')
if len(event_id) == 0:
event_id = 'e' + str(self.model.getNumEvents())
self.check(e1.setId(event_id), 'add id to event')
if self.document.getLevel()==3 or (self.document.getLevel()==2 \
and self.document.getVersion()==4):
self.check(e1.setUseValuesFromTriggerTime(True),
'set use values from trigger time')
tri = e1.createTrigger()
self.check(tri, 'add trigger to event')
tri_ast = libsbml.parseL3Formula(trigger)
self.check(tri.setMath(tri_ast), 'add formula to trigger')
if self.document.getLevel() == 3:
self.check(tri.setPersistent(persistent),
'set persistence of trigger')
self.check(tri.setInitialValue(initial_value),
'set initial value of trigger')
de = e1.createDelay()
if self.document.getLevel() == 3:
k = self.addParameter(event_id + 'Delay', delay,
self.model.getTimeUnits())
else:
k = self.addParameter(event_id + 'Delay', delay, 'time')
self.check(de, 'add delay to event')
delay_ast = libsbml.parseL3Formula(k.getId())
self.check(de.setMath(delay_ast), 'set formula for delay')
for a in assignments.keys():
assign = e1.createEventAssignment()
self.check(assign, 'add event assignment to event')
self.check(assign.setVariable(a),
'add variable to event assignment')
val_ast = libsbml.parseL3Formula(assignments.get(a))
self.check(assign.setMath(val_ast),
'add value to event assignment')
if self.document.getLevel() == 3:
pri = e1.createPriority()
pri_ast = libsbml.parseL3Formula(str(priority))
self.check(pri.setMath(pri_ast), 'add priority to event')
return e1
def addAssignmentRule(self, var, math):
"""To assign a state variable with an expression"""
r = self.model.createAssignmentRule()
self.check(r, "create assignment rule r")
self.check(r.setVariable(var), "set assignment rule variable")
math_ast = libsbml.parseL3Formula(math)
self.check(r.setMath(math_ast), "set assignment rule equation")
return r
def addInitialAssignment(self, symbol, math):
if self.document.getLevel() == 2 and self.document.getVersion() == 1:
raise SystemExit('Error: InitialAssignment does not exist for \
this level and version.')
a = self.model.createInitialAssignment()
self.check(a, 'create initial assignment a')
self.check(a.setSymbol(symbol), 'set initial assignment a symbol')
math_ast = libsbml.parseL3Formula(math)
self.check(a.setMath(math_ast), 'set initial assignment a math')
return a
def addInitialAssignment(self, symbol, math):
if self.document.getLevel() == 2 and self.document.getVersion() == 1:
raise SystemExit('Error: InitialAssignment does not exist for \
this level and version.')
a = self.model.createInitialAssignment()
self.check(a, 'create initial assignment a')
self.check(a.setSymbol(symbol), 'set initial assignment a symbol')
math_ast = libsbml.parseL3Formula(math)
self.check(a.setMath(math_ast), 'set initial assignment a math')
return a
def addEvent(self, trigger, assignments, persistent=True, \
initial_value=False, priority=0, delay=0, event_id=''):
e1 = self.model.createEvent()
self.check(e1, 'create event')
if len(event_id) == 0:
event_id = 'e' + str(self.model.getNumEvents())
self.check(e1.setId(event_id), 'add id to event')
if self.document.getLevel()==3 or (self.document.getLevel()==2 \
and self.document.getVersion()==4):
self.check(e1.setUseValuesFromTriggerTime(True), 'set use values from trigger time')
tri = e1.createTrigger()
self.check(tri, 'add trigger to event')
tri_ast = libsbml.parseL3Formula(trigger)
self.check(tri.setMath(tri_ast), 'add formula to trigger')
if self.document.getLevel() == 3:
self.check(tri.setPersistent(persistent), 'set persistence of trigger')
self.check(tri.setInitialValue(initial_value), 'set initial value of trigger')
de = e1.createDelay()
if self.document.getLevel() == 3:
k = self.addParameter(event_id+'Delay', delay, self.model.getTimeUnits())
else:
k = self.addParameter(event_id+'Delay', delay, 'time')
self.check(de, 'add delay to event')
delay_ast = libsbml.parseL3Formula(k.getId())
self.check(de.setMath(delay_ast), 'set formula for delay')
for a in assignments.keys():
assign = e1.createEventAssignment()
self.check(assign, 'add event assignment to event')
self.check(assign.setVariable(a), 'add variable to event assignment')
val_ast = libsbml.parseL3Formula(assignments.get(a))
self.check(assign.setMath(val_ast), 'add value to event assignment')
if self.document.getLevel() == 3:
pri = e1.createPriority()
pri_ast = libsbml.parseL3Formula(str(priority))
self.check(pri.setMath(pri_ast), 'add priority to event')
return e1
def addRateRule(self, var, math, rr_id=''):
r = self.model.createRateRule()
self.check(r, 'create rate rule r')
if len(rr_id) == 0:
rr_id = 'Rate' + str(self.model.getNumRules())
r.setIdAttribute(rr_id)
print('rr_id=', r.getIdAttribute())
#self.check(r.setId(rr_id), 'set rate rule id')
self.check(r.setVariable(var), 'set rate rule variable')
math_ast = libsbml.parseL3Formula(math)
self.check(r.setMath(math_ast), 'set rate rule equation')
return r
def addInitialAssignment(self, symbol, math):
"""Describe the initial value of the variable in terms of
other variables or parameters.
"""
if self.document.getLevel() == 2 and self.document.getVersion() == 1:
raise SystemExit("Error: InitialAssignment does not exist for \
this level and version.")
a = self.model.createInitialAssignment()
self.check(a, "create initial assignment a")
self.check(a.setSymbol(symbol), "set initial assignment a symbol")
math_ast = libsbml.parseL3Formula(math)
self.check(a.setMath(math_ast), "set initial assignment a math")
return a
def addRateRule(self, var, math, rr_id=""):
"""Describe the derivative of the state variable wrt time as an expression."""
r = self.model.createRateRule()
self.check(r, "create rate rule r")
if len(rr_id) == 0:
rr_id = "Rate" + str(self.model.getNumRules())
r.setIdAttribute(rr_id)
# print("rr_id=", r.getIdAttribute())
# self.check(r.setId(rr_id), 'set rate rule id')
self.check(r.setVariable(var), "set rate rule variable")
math_ast = libsbml.parseL3Formula(math)
self.check(r.setMath(math_ast), "set rate rule equation")
return r
def addReaction(self,
reactants,
products,
expression,
local_params={},
rxn_id=''):
r1 = self.model.createReaction()
self.check(r1, 'create reaction')
if len(rxn_id) == 0:
rxn_id = 'v' + str(self.model.getNumReactions())
self.check(r1.setId(rxn_id), 'set reaction id')
self.check(r1.setReversible(False), 'set reaction reversibility flag')
self.check(r1.setFast(False), 'set reaction "fast" attribute')
for re in reactants:
if re is not None and '$' in re:
re.translate(None, '$')
re_split = re.split()
if len(re_split) == 1:
sto = 1.0
re_id = re
elif len(re_split) == 2 and re_split[0].isdigit():
sto = float(re_split[0])
re_id = re_split[1]
else:
err_msg = 'Error: reactants must be listed in format \'S\' or \'(float)\' S\''
raise SystemExit(err_msg)
s1 = self.model.getSpecies(re_id)
species_ref1 = r1.createReactant()
self.check(species_ref1, 'create reactant')
self.check(species_ref1.setSpecies(s1.getId()), \
'assign reactant species')
self.check(species_ref1.setStoichiometry(sto), \
'assign reactant stoichiometry')
if self.document.getLevel() == 3:
self.check(species_ref1.setConstant(True), \
'set "constant" on species ref 1')
for pro in products:
if pro is not None and '$' in pro:
pro.translate(None, '$')
pro_split = pro.split()
if len(pro_split) == 1:
sto = 1.0
pro_id = pro
elif len(pro_split) == 2:
sto = float(pro_split[0])
pro_id = pro_split[1]
else:
err_msg = 'Error: products must be listed in format \'S\' or \'(float)\' S\''
raise SystemExit(err_msg)
s2 = self.model.getSpecies(pro_id)
species_ref2 = r1.createProduct()
self.check(species_ref2, 'create product')
self.check(species_ref2.setSpecies(s2.getId()), \
'assign product species')
self.check(species_ref2.setStoichiometry(sto), \
'set product stoichiometry')
if self.document.getLevel() == 3:
self.check(species_ref2.setConstant(True), \
'set "constant" on species ref 2')
math_ast = libsbml.parseL3Formula(expression)
self.check(math_ast, 'create AST for rate expression')
kinetic_law = r1.createKineticLaw()
self.check(kinetic_law, 'create kinetic law')
self.check(kinetic_law.setMath(math_ast), 'set math on kinetic law')
for param in local_params.keys():
val = local_params.get(param)
if self.document.getLevel() == 3:
p = kinetic_law.createLocalParameter()
else:
p = kinetic_law.createParameter()
self.check(p, 'create local parameter')
self.check(p.setId(param), 'set id of local parameter')
self.check(p.setValue(val), 'set value of local parameter')
return r1
def addReaction(self, reactants, products, expression, local_params={}, rxn_id=''):
r1 = self.model.createReaction()
self.check(r1, 'create reaction')
if len(rxn_id) == 0:
rxn_id = 'v' + str(self.model.getNumReactions())
self.check(r1.setId(rxn_id), 'set reaction id')
self.check(r1.setReversible(False), 'set reaction reversibility flag')
self.check(r1.setFast(False), 'set reaction "fast" attribute')
for re in reactants:
if re is not None and '$' in re:
re.translate(None, '$')
re_split = re.split()
if len(re_split) == 1:
sto = 1.0
re_id = re
elif len(re_split) == 2 and re_split[0].isdigit():
sto = float(re_split[0])
re_id = re_split[1]
else:
err_msg = 'Error: reactants must be listed in format \'S\' or \'(float)\' S\''
raise SystemExit(err_msg)
s1 = self.model.getSpecies(re_id)
species_ref1 = r1.createReactant()
self.check(species_ref1, 'create reactant')
self.check(species_ref1.setSpecies(s1.getId()), \
'assign reactant species')
self.check(species_ref1.setStoichiometry(sto), \
'assign reactant stoichiometry')
if self.document.getLevel() == 3:
self.check(species_ref1.setConstant(True), \
'set "constant" on species ref 1')
for pro in products:
if pro is not None and '$' in pro:
pro.translate(None, '$')
pro_split = pro.split()
if len(pro_split) == 1:
sto = 1.0
pro_id = pro
elif len(pro_split) == 2:
sto = float(pro_split[0])
pro_id = pro_split[1]
else:
err_msg = 'Error: products must be listed in format \'S\' or \'(float)\' S\''
raise SystemExit(err_msg)
s2 = self.model.getSpecies(pro_id)
species_ref2 = r1.createProduct()
self.check(species_ref2, 'create product')
self.check(species_ref2.setSpecies(s2.getId()), \
'assign product species')
self.check(species_ref2.setStoichiometry(sto), \
'set product stoichiometry')
if self.document.getLevel() == 3:
self.check(species_ref2.setConstant(True), \
'set "constant" on species ref 2')
math_ast = libsbml.parseL3Formula(expression)
self.check(math_ast, 'create AST for rate expression')
kinetic_law = r1.createKineticLaw()
self.check(kinetic_law, 'create kinetic law')
self.check(kinetic_law.setMath(math_ast), 'set math on kinetic law')
for param in local_params.keys():
val = local_params.get(param)
if self.document.getLevel() == 3:
p = kinetic_law.createLocalParameter()
else:
p = kinetic_law.createParameter()
self.check(p, 'create local parameter')
self.check(p.setId(param), 'set id of local parameter')
self.check(p.setValue(val), 'set value of local parameter')
return r1
def addEvent(
self,
trigger,
assignments,
persistent=True,
initial_value=False,
priority=0,
delay=0,
event_id="",
):
"""Add event supplied with when an event is triggered and
what happens using assignments in a dictionary.
:param trigger: define when an event is triggered (logical expression)
:type trigger: str
:param assignments: keys are the variables to be modified and the values are the new values
:type assignments: dict
:param persistent: determine if the event will still be executed if trigger turns from
True to False
:type persistent: boolean
:param initial_value: value of trigger before t=0
:type initial_value: boolean
:param priority: determine which event is executed, event with larger priority is executed
:type priority: float
:param delay: time between when the event is triggered and the assignment is implemented
:type delay: float
:param event_id: id of the event
:type event_id: str
"""
e1 = self.model.createEvent()
self.check(e1, "create event")
if len(event_id) == 0:
event_id = "e" + str(self.model.getNumEvents())
self.check(e1.setId(event_id), "add id to event")
if self.document.getLevel() == 3 or (self.document.getLevel() == 2 and
self.document.getVersion() == 4):
self.check(e1.setUseValuesFromTriggerTime(True),
"set use values from trigger time")
tri = e1.createTrigger()
self.check(tri, "add trigger to event")
tri_ast = libsbml.parseL3Formula(trigger)
self.check(tri.setMath(tri_ast), "add formula to trigger")
if self.document.getLevel() == 3:
self.check(tri.setPersistent(persistent),
"set persistence of trigger")
self.check(tri.setInitialValue(initial_value),
"set initial value of trigger")
de = e1.createDelay()
if self.document.getLevel() == 3:
k = self.addParameter(event_id + "Delay", delay,
self.model.getTimeUnits())
else:
k = self.addParameter(event_id + "Delay", delay, "time")
self.check(de, "add delay to event")
delay_ast = libsbml.parseL3Formula(k.getId())
self.check(de.setMath(delay_ast), "set formula for delay")
for a in assignments.keys():
assign = e1.createEventAssignment()
self.check(assign, "add event assignment to event")
self.check(assign.setVariable(a),
"add variable to event assignment")
val_ast = libsbml.parseL3Formula(assignments.get(a))
self.check(assign.setMath(val_ast),
"add value to event assignment")
if self.document.getLevel() == 3:
pri = e1.createPriority()
pri_ast = libsbml.parseL3Formula(str(priority))
self.check(pri.setMath(pri_ast), "add priority to event")
return e1
def addReaction(self,
reactants,
products,
expression,
local_params=None,
rxn_id=""):
"""Create reaction provided with reactants and products in lists
:param reactants: list of species id for reactants
:type reactants: list
:param products: list of species id for products
:type products: list
:param expression: reaction rate expression
:type expression: str
:param local_params: keys are the param id and values are their respective values
:type local_params: dict
:param rxn_id: id for the reaction
:type rxn_id: str, optional
"""
r1 = self.model.createReaction()
self.check(r1, "create reaction")
if len(rxn_id) == 0:
rxn_id = "v" + str(self.model.getNumReactions())
self.check(r1.setId(rxn_id), "set reaction id")
self.check(r1.setReversible(False), "set reaction reversibility flag")
self.check(r1.setFast(False), 'set reaction "fast" attribute')
for re in reactants:
if re is not None and "$" in re:
re.translate(None, "$")
re_split = re.split()
if len(re_split) == 1:
sto = 1.0
re_id = re
elif len(re_split) == 2 and re_split[0].isdigit():
sto = float(re_split[0])
re_id = re_split[1]
else:
err_msg = (
"Error: reactants must be listed in format 'S' or '(float)' S'"
)
raise SystemExit(err_msg)
s1 = self.model.getSpecies(re_id)
species_ref1 = r1.createReactant()
self.check(species_ref1, "create reactant")
self.check(species_ref1.setSpecies(s1.getId()),
"assign reactant species")
self.check(species_ref1.setStoichiometry(sto),
"assign reactant stoichiometry")
if self.document.getLevel() == 3:
self.check(species_ref1.setConstant(True),
'set "constant" on species ref 1')
for pro in products:
if pro is not None and "$" in pro:
pro.translate(None, "$")
pro_split = pro.split()
if len(pro_split) == 1:
sto = 1.0
pro_id = pro
elif len(pro_split) == 2:
sto = float(pro_split[0])
pro_id = pro_split[1]
else:
err_msg = "Error: products must be listed in format 'S' or '(float)' S'"
raise SystemExit(err_msg)
s2 = self.model.getSpecies(pro_id)
species_ref2 = r1.createProduct()
self.check(species_ref2, "create product")
self.check(species_ref2.setSpecies(s2.getId()),
"assign product species")
self.check(species_ref2.setStoichiometry(sto),
"set product stoichiometry")
if self.document.getLevel() == 3:
self.check(species_ref2.setConstant(True),
'set "constant" on species ref 2')
math_ast = libsbml.parseL3Formula(expression)
self.check(math_ast, "create AST for rate expression")
kinetic_law = r1.createKineticLaw()
self.check(kinetic_law, "create kinetic law")
self.check(kinetic_law.setMath(math_ast), "set math on kinetic law")
if local_params is not None:
for param in local_params.keys():
val = local_params.get(param)
if self.document.getLevel() == 3:
p = kinetic_law.createLocalParameter()
else:
p = kinetic_law.createParameter()
self.check(p, "create local parameter")
self.check(p.setId(param), "set id of local parameter")
self.check(p.setValue(val), "set value of local parameter")
return r1
