def binds(name_a, name_b):
"""Rule for 'A binds B'."""
A = new_variable(nickname=name_a)
B = new_variable(nickname=name_b)
return predicate.Exists(predicate.Implies(predicate.Named(A, name_a),
predicate.Implies(predicate.Named(B, name_b),
predicate.Not(predicate.And(predicate.PreLink(A, B)),
predicate.PostLink(A, B)))))
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)))))
print ii.get_predicate()
print "\nPredicate III: MEK directly activates ERK in a single step.\nTranslated to z3:"
iii = directly_activates("MEK", "ERK")
print iii.get_predicate()
print "\nEach of these predicates is satisfiable (True) on their own: checking..."
assert i.check_sat()
print i.check_sat()
assert ii.check_sat()
print ii.check_sat()
assert iii.check_sat()
print iii.check_sat()
print "\nI and II are satisfiable together: checking And(I, II)..."
and_i_ii = predicate.And(i, ii)
assert and_i_ii.check_sat()
print and_i_ii.check_sat()
print "\nI and II imply III: checking Implies(And(I, II), III)..."
implication = predicate.Implies(and_i_ii, iii)
assert implication.check_sat()
print implication.check_sat()
print "\nI and II and III are satisfiable together: checking And(I, II, III)..."
and_i_ii_iii = predicate.And(i, ii, iii)
assert and_i_ii_iii.check_sat()
print and_i_ii_iii.check_sat()
print "\nHector's examples"