def phosphorylated_is_active(name_b):
"""
Macro for 'phosphorylated "B" is active'.
"""
# Forall Model, *Forall* Rule in Model, Forall B, Named B named_b => and(...)
B = new_variable(nickname=name_b)
intp = datatypes.new_interpretation()
return predicate.ForAll(predicate.Implies(predicate.Named(B, name_b),
predicate.And(predicate.Implies(predicate.PreLabeled(B, PHOSPHORYLATED),
predicate.PreLabeled(B, ACTIVE)),
predicate.Implies(predicate.PostLabeled(B, PHOSPHORYLATED),
predicate.PostLabeled(B, ACTIVE)))))
def directly_activates(name_a, name_b):
"""
Macro for 'activated "A" activates "B"'.
"""
# Forall Model, Exists Rule in Model, [...]
A = new_variable(nickname=name_a)
B = new_variable(nickname=name_b)
intp = datatypes.new_interpretation()
return predicate.Exists(predicate.Implies(predicate.Named(A, name_a),
predicate.Implies(predicate.Named(B, name_b),
predicate.And(predicate.PreLabeled(A, ACTIVE),
predicate.PreUnlabeled(B, ACTIVE),
predicate.PostLabeled(A, ACTIVE),
predicate.PostLabeled(B, ACTIVE)))))
def directly_phosphorylates(name_a, name_b):
"""
Macro for 'activated "A" phosphorylates "B"'.
"""
A = new_variable(nickname=name_a)
B = new_variable(nickname=name_b)
# Okay, so what I actually want this to say is as follows:
# Forall Model, Exists Rule in Model, reaction stuff holds over rule
# reaction stuff = Forall A B, Named A name_a /\ Named B name_b => prelabeled etc
intp = datatypes.new_interpretation()
return predicate.Exists(predicate.Implies(predicate.Named(A, name_a),
predicate.Implies(predicate.Named(B, name_b),
predicate.And(predicate.PreLabeled(A, ACTIVE),
predicate.PreUnlabeled(B, PHOSPHORYLATED),
predicate.PostLabeled(A, ACTIVE),
predicate.PostLabeled(B, PHOSPHORYLATED)))))
def setUp(self):
self.submodel = datatypes.new_model()
self.interpretation = datatypes.new_interpretation()
def get_predicate(self):
# returns a z3 predicate
modelset = new_modelset()
interpretation = new_interpretation()
predicate = self._assert(modelset, interpretation, None, None)
return predicate
def get_predicate(self):
# returns a z3 predicate
modelset = new_modelset()
interpretation = new_interpretation()
predicate = self._assert(modelset, interpretation, None, None)
return predicate