def make_predicate(statement):
if isinstance(statement, indra.statements.Phosphorylation):
# <enzyme> phosphorylates <substrate>
# str() because sometimes these are Unicode
enzyme = str(statement.enz.name)
substrate = str(statement.sub.name)
return macros.directly_phosphorylates(enzyme, substrate)
elif isinstance(statement, indra.statements.ActivityActivity):
# <enzyme> activates <substrate>
upstream = str(statement.subj.name)
downstream = str(statement.obj.name)
if statement.subj_activity == 'Activity' and statement.obj_activity == 'Activity':
return macros.directly_activates(upstream, downstream)
else:
raise NotImplementedError(str(statement))
elif isinstance(statement, indra.statements.ActivityModification):
name = str(statement.monomer.name)
return macros.phosphorylated_is_active(name)
raise NotImplementedError(str(statement))
def make_predicate(statement):
if isinstance(statement, indra.statements.Phosphorylation):
# <enzyme> phosphorylates <substrate>
# str() because sometimes these are Unicode
enzyme = statement.enz.name.encode('utf-8')
substrate = statement.sub.name.encode('utf-8')
return macros.directly_phosphorylates(enzyme, substrate)
elif isinstance(statement, indra.statements.Activation):
# <enzyme> activates <substrate>
upstream = statement.subj.name.encode('utf-8')
downstream = statement.obj.name.encode('utf-8')
if statement.subj_activity == 'activity' and statement.obj_activity == 'activity':
return macros.directly_activates(upstream, downstream)
else:
raise NotImplementedError(str(statement))
elif isinstance(statement, indra.statements.ActiveForm):
if len(statement.mods) == 1 and \
statement.mods[0].mod_type == 'phosphorylation' and \
statement.is_active:
name = statement.agent.name.encode('utf-8')
return macros.phosphorylated_is_active(name)
raise NotImplementedError(str(statement))
def make_predicate(statement):
if isinstance(statement, indra.statements.Phosphorylation):
# <enzyme> phosphorylates <substrate>
# str() because sometimes these are Unicode
enzyme = statement.enz.name.encode('utf-8')
substrate = statement.sub.name.encode('utf-8')
return macros.directly_phosphorylates(enzyme, substrate)
elif isinstance(statement, indra.statements.Activation):
# <enzyme> activates <substrate>
upstream = statement.subj.name.encode('utf-8')
downstream = statement.obj.name.encode('utf-8')
if statement.subj_activity == 'activity' and statement.obj_activity == 'activity':
return macros.directly_activates(upstream, downstream)
else:
raise NotImplementedError(str(statement))
elif isinstance(statement, indra.statements.ActiveForm):
if len(statement.mods) == 1 and \
statement.mods[0].mod_type == 'phosphorylation' and \
statement.is_active:
name = statement.agent.name.encode('utf-8')
return macros.phosphorylated_is_active(name)
raise NotImplementedError(str(statement))
from macros import directly_phosphorylates, directly_activates, phosphorylated_is_active
import predicate
from solver import solver
import z3
# Sanity checks.
assert not predicate.Bottom().check_sat()
assert predicate.Top().check_sat()
assert not predicate.And(predicate.Bottom(), predicate.Top()).check_sat()
assert not predicate.ForAll(predicate.Bottom()).check_sat()
assert predicate.ForAll(predicate.Top()).check_sat()
assert not predicate.Exists(predicate.Bottom()).check_sat()
assert predicate.Exists(predicate.Top()).check_sat()
print "Predicate I: MEK directly phosphorylates ERK in a single step.\nTranslated to z3:"
i = directly_phosphorylates("MEK", "ERK")
print i.get_predicate()
print "\nPredicate II: ERK, when phosphorylated, is always active.\nTranslated to z3:"
ii = phosphorylated_is_active("ERK")
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()
import predicate
from solver import solver
import z3
# Sanity checks.
assert not predicate.Bottom().check_sat()
assert predicate.Top().check_sat()
assert not predicate.And(predicate.Bottom(), predicate.Top()).check_sat()
assert not predicate.ForAll(predicate.Bottom()).check_sat()
assert predicate.ForAll(predicate.Top()).check_sat()
assert not predicate.Exists(predicate.Bottom()).check_sat()
assert predicate.Exists(predicate.Top()).check_sat()
print "Predicate I: MEK directly phosphorylates ERK in a single step.\nTranslated to z3:"
i = directly_phosphorylates("MEK", "ERK")
print i.get_predicate()
print "\nPredicate II: ERK, when phosphorylated, is always active.\nTranslated to z3:"
ii = phosphorylated_is_active("ERK")
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()
