329 lines
12 KiB
Python
329 lines
12 KiB
Python
from rs import *
|
|
from smt import *
|
|
import rs_examples
|
|
from logics import *
|
|
import sys
|
|
import resource
|
|
|
|
def run_tests():
|
|
|
|
# test_extended_automaton()
|
|
# process()
|
|
# heat_shock_response()
|
|
scalable_chain(print_system=True)
|
|
|
|
def heat_shock_response(print_system=True):
|
|
|
|
stress_temp = 42
|
|
max_temp = 50
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("hsp",1))
|
|
r.add_bg_set_entity(("hsf",1))
|
|
r.add_bg_set_entity(("hsf2",1))
|
|
r.add_bg_set_entity(("hsf3",1))
|
|
r.add_bg_set_entity(("hse",1))
|
|
r.add_bg_set_entity(("mfp",1))
|
|
r.add_bg_set_entity(("prot",1))
|
|
r.add_bg_set_entity(("hsf3:hse",1))
|
|
r.add_bg_set_entity(("hsp:mfp",1))
|
|
r.add_bg_set_entity(("hsp:hsf",1))
|
|
r.add_bg_set_entity(("temp",max_temp))
|
|
r.add_bg_set_entity(("heat",1))
|
|
r.add_bg_set_entity(("cool",1))
|
|
|
|
r.add_reaction([("hsf",1)], [("hsp",1)], [("hsf3",1)])
|
|
r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)])
|
|
r.add_reaction([("hsf3",1)], [("hse",1),("hsp",1)],[("hsf",1)])
|
|
r.add_reaction([("hsf3",1),("hsp",1),("mfp",1)], [("hse",1)], [("hsf",1)])
|
|
r.add_reaction([("hsf3",1),("hse",1)], [("hsp",1)], [("hsf3:hse",1)])
|
|
r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[], [("hsf3:hse",1)])
|
|
r.add_reaction([("hse",1)], [("hsf3",1)], [("hse",1)])
|
|
r.add_reaction([("hsp",1),("hsf3",1),("hse",1)], [("mfp",1)], [("hse",1)])
|
|
r.add_reaction([("hsf3:hse",1)], [("hsp",1)], [("hsp",1),("hsf3:hse",1)])
|
|
r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[], [("hsp",1),("hsf3:hse",1)])
|
|
r.add_reaction([("hsf",1),("hsp",1)], [("mfp",1)], [("hsp:hsf",1)])
|
|
r.add_reaction([("hsp:hsf",1),("temp",stress_temp)],[], [("hsf",1),("hsp",1)])
|
|
r.add_reaction([("hsp:hsf",1)], [("temp",stress_temp)],[("hsp:hsf",1)])
|
|
r.add_reaction([("hsp",1),("hsf3:hse",1)], [("mfp",1)], [("hse",1),("hsp:hsf",1)])
|
|
r.add_reaction([("temp",stress_temp),("prot",1)], [], [("mfp",1),("prot",1)])
|
|
r.add_reaction([("prot",1)], [("temp",stress_temp)], [("prot",1)])
|
|
r.add_reaction([("hsp",1),("mfp",1)], [], [("hsp:mfp",1)])
|
|
r.add_reaction([("mfp",1)], [("hsp",1)], [("mfp",1)])
|
|
r.add_reaction([("hsp:mfp",1)], [], [("hsp",1),("prot",1)])
|
|
|
|
r.add_reaction_inc("temp", "heat", [("temp",1)],[("temp",max_temp)])
|
|
r.add_reaction_dec("temp", "cool", [("temp",1)],[])
|
|
|
|
r.add_permanency("temp",[("heat",1),("cool",1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1")
|
|
c.add_transition("1", [("cool",1)], "1")
|
|
c.add_transition("1", [("heat",1)], "1")
|
|
c.add_transition("1", [], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r,c)
|
|
|
|
if print_system:
|
|
rc.show()
|
|
|
|
# prop_req = [("hsp:hsf",1),("hse",1),("prot",1)]
|
|
# prop_block = [("temp",stress_temp)]
|
|
# prop_req = [ ("mfp",1) ]
|
|
# prop_block = [ ]
|
|
# prop = (prop_req,prop_block)
|
|
# rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
|
|
#
|
|
# f_reach_mfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("mfp") > 0) )
|
|
|
|
smt_rsc = SmtCheckerRSC(rc)
|
|
|
|
# (1) if we keep increasing the temperature the protein will eventually misfold
|
|
# f_mfp_when_heating = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("mfp") > 0) )
|
|
# )
|
|
# smt_rsc.check_rsltl(formula=f_mfp_when_heating)
|
|
|
|
# (2) when heating, we finally exceed the stress_temp
|
|
f_2 = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("temp") > stress_temp))
|
|
)
|
|
smt_rsc.check_rsltl(formula=f_2)
|
|
|
|
# smt_rsc.check_reachability(prop,max_level=40)
|
|
|
|
def state_translate_rsc2rs(p):
|
|
return [e[0] + "#" + str(e[1]) for e in p]
|
|
|
|
|
|
def scalable_chain(print_system=False):
|
|
|
|
if len(sys.argv) < 1+3:
|
|
print("arguments: <chainLen> <maxConc> <formulaNumber>")
|
|
exit(1)
|
|
|
|
chainLen=int(sys.argv[1]) # chain length
|
|
maxConc=int(sys.argv[2]) # depth (max concentration)
|
|
formula_number=int(sys.argv[3])
|
|
|
|
if chainLen < 1 or maxConc < 1:
|
|
print("be reasonable")
|
|
exit(1)
|
|
if not formula_number in range(1,4+1):
|
|
print("formulaNumber must be in 1..4")
|
|
exit(1)
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("inc",1))
|
|
r.add_bg_set_entity(("dec",1))
|
|
|
|
for i in range(1,chainLen+1):
|
|
r.add_bg_set_entity(("e_" + str(i),maxConc))
|
|
|
|
for i in range(1,chainLen+1):
|
|
ent = "e_" + str(i)
|
|
r.add_reaction_inc(ent, "inc", [(ent, 1)],[(ent,maxConc)])
|
|
r.add_reaction_dec(ent, "dec", [(ent, 1)],[])
|
|
if i < chainLen:
|
|
r.add_reaction([(ent,maxConc)],[],[("e_"+str(i+1),1)])
|
|
|
|
r.add_reaction([("e_" + str(chainLen),maxConc)],[("dec",1)],[("e_" + str(chainLen),maxConc)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("init")
|
|
c.add_state("working")
|
|
c.add_transition("init", [("e_1",1),("inc",1)], "working")
|
|
c.add_transition("working", [("inc",1)], "working")
|
|
|
|
rc = ReactionSystemWithAutomaton(r,c)
|
|
|
|
if print_system:
|
|
rc.show()
|
|
|
|
smt_rsc = SmtCheckerRSC(rc)
|
|
|
|
if formula_number == 1:
|
|
f_1 = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, (BagDescription.f_entity('e_'+str(chainLen)) >= maxConc) )
|
|
smt_rsc.check_rsltl(formula=f_1)
|
|
elif formula_number == 2:
|
|
f_tmp = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, (BagDescription.f_entity('e_'+str(chainLen)) == maxConc) )
|
|
for i in range(chainLen-1,0,-1):
|
|
f_tmp = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, f_tmp & (BagDescription.f_entity('e_'+str(i)) == maxConc) )
|
|
f_2 = f_tmp
|
|
smt_rsc.check_rsltl(formula=f_2)
|
|
elif formula_number == 3:
|
|
f_3 = Formula_rsLTL.f_G( BagDescription.f_TRUE(),
|
|
Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('e_1') == 1),
|
|
Formula_rsLTL.f_F(
|
|
BagDescription.f_entity("inc") > 0,
|
|
(BagDescription.f_entity('e_'+str(i)) == maxConc)
|
|
)
|
|
)
|
|
)
|
|
smt_rsc.check_rsltl(formula=f_3)
|
|
elif formula_number == 4:
|
|
f_4 = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0 , BagDescription.f_entity('e_1') == maxConc )
|
|
smt_rsc.check_rsltl(formula=f_4)
|
|
|
|
###########################################################################
|
|
|
|
time=0
|
|
mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
|
|
filename_t="bench_rsc_F" + str(formula_number) + "_time.log"
|
|
filename_m="bench_rsc_F" + str(formula_number) + "_mem.log"
|
|
time=smt_rsc.get_verification_time()
|
|
|
|
f=open(filename_t, 'a')
|
|
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n"
|
|
f.write(log_str)
|
|
f.close()
|
|
|
|
f=open(filename_m, 'a')
|
|
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n"
|
|
f.write(log_str)
|
|
f.close()
|
|
|
|
|
|
def test_rsLTL():
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("inc",2))
|
|
r.add_bg_set_entity(("ent1",1))
|
|
r.add_bg_set_entity(("ent2",5))
|
|
r.add_reaction([("ent2",1),("inc",1)],[],[("ent2",2)])
|
|
r.add_reaction([("ent2",2)],[],[("ent2",2)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("init")
|
|
c.add_state("working")
|
|
c.add_transition("init", [("ent2",1),("inc",1)], "working")
|
|
c.add_transition("working", [("inc",1)], "working")
|
|
|
|
# x = ( Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_bag( ~((BagDescription.f_entity("ent1") == 3) | (BagDescription.f_entity("ent2") < 3)) ) ) ) & Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_bag( ~((BagDescription.f_entity("ent3") == 1) ) ) )
|
|
x = Formula_rsLTL.f_G((BagDescription.f_entity("inc") > 0), (BagDescription.f_entity("ent1") == 3) | (BagDescription.f_entity("ent2") < 3))
|
|
|
|
#x = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("ent2") == 2) )
|
|
|
|
print(x)
|
|
|
|
rc = ReactionSystemWithAutomaton(r,c)
|
|
rc.show()
|
|
|
|
checker = SmtCheckerRSC(rc)
|
|
checker.check_rsltl(formula=x)
|
|
|
|
# checker.dummy_unroll(10)
|
|
# e = rsLTL_Encoder(checker)
|
|
# print(checker.get_loop_encodings())
|
|
# print(e.encode(x, 0, 10))
|
|
|
|
def test_extended_automaton():
|
|
|
|
r = ReactionSystem()
|
|
r.add_bg_set_entity("a")
|
|
r.add_bg_set_entity("b")
|
|
r.add_bg_set_entity("inc")
|
|
r.add_bg_set_entity("dec")
|
|
r.add_bg_set_entity("decx")
|
|
r.add_bg_set_entity("baam")
|
|
|
|
c1 = ExtendedContextAutomaton(r)
|
|
c1.add_init_state("init")
|
|
c1.name = "catest"
|
|
c1.add_state("working")
|
|
c1.add_action("act1")
|
|
c1.add_action("act2")
|
|
c1.add_transition("init", ["act1", "act2"], (["a"],["b"],["inc","dec"]), "working")
|
|
c1.add_transition("working", ["act2"], ([],[],["inc"]), "working")
|
|
|
|
c2 = ExtendedContextAutomaton(r)
|
|
c2.add_init_state("init")
|
|
c2.name = "c2"
|
|
c2.add_state("working")
|
|
c2.add_action("act1")
|
|
c2.add_action("act2")
|
|
c2.add_transition("init", ["act1", "act2"], ([],[],["inc"]), "working")
|
|
c2.add_transition("working", ["act2"], ([],[],["inc"]), "working")
|
|
|
|
c3 = ExtendedContextAutomaton(r)
|
|
c3.add_init_state("init")
|
|
c3.name = "c3"
|
|
c3.add_state("working")
|
|
c3.add_action("act1")
|
|
c3.add_transition("init", ["act1"], ([],[],["inc"]), "working")
|
|
|
|
c4 = ExtendedContextAutomaton(r)
|
|
c4.add_init_state("init")
|
|
c4.name = "c4"
|
|
c4.add_state("w")
|
|
c4.add_action("action_x")
|
|
c4.add_transition("init", ["action_x"], ([],[],["baam"]), "w")
|
|
#
|
|
# c4 = ExtendedContextAutomaton(r)
|
|
# c4.add_init_state("init")
|
|
# c4.name = "c4"
|
|
# c4.add_state("working")
|
|
# c4.add_action("act1")
|
|
# c4.add_action("act42")
|
|
# c4.add_transition("init", ["act1", "act42"], ([],[],["inc"]), "working")
|
|
# c4.add_transition("working", ["act42"], ([],[],["inc"]), "working")
|
|
#
|
|
# c5 = ExtendedContextAutomaton(r)
|
|
# c5.add_init_state("init")
|
|
# c5.name = "c5"
|
|
# c5.add_state("working")
|
|
# c5.add_action("act1")
|
|
# c5.add_action("act2")
|
|
# c5.add_transition("init", ["act1", "act2"], ([],[],["inc"]), "working")
|
|
# c5.add_transition("working", ["act2"], ([],[],["inc"]), "working")
|
|
|
|
na = NetworkOfContextAutomata(r, [c1,c2,c3,c4])
|
|
|
|
rna = ReactionSystemWithNetworkOfAutomata(r,na)
|
|
|
|
rna.show()
|
|
|
|
checker = SmtCheckerRSNA(rna)
|
|
|
|
checker.check_reachability([])
|
|
|
|
def process():
|
|
|
|
# rs_examples.run_counter_exp()
|
|
rs_examples.chain_reaction(print_system=True)
|
|
# rs_examples.heat_shock_response()
|
|
|
|
|
|
|
|
# RS:
|
|
# rsca = rs_examples.ca_toy_ex1()
|
|
# rsca.show()
|
|
# smt = SmtCheckerRS(rsca)
|
|
# smt.check_reachability(rs_examples.ca_toy_ex1_property1(), print_time=True)
|
|
|
|
# rsca = rs_examples.ca_bitctr(N)
|
|
# rsca.show(True)
|
|
# smt = SmtCheckerRS(rsca)
|
|
# smt.check_reachability(rs_examples.ca_bitctr_property(N), print_time=True)
|
|
|
|
# Distributed RS:
|
|
#drs = rs_examples.drs_mutex(N)
|
|
#drs.show()
|
|
|
|
#smt = SmtCheckerDistribRS(drs,debug_level=0)
|
|
#smt.check_reachability(rs_examples.drs_mutex_property1(N),
|
|
# exclusive_state=False,
|
|
# max_level=10,
|
|
# print_time=True,
|
|
# print_mem=True)
|
|
|
|
# drs = rs_examples.drs_toy_ex1()
|
|
# drs.show()
|
|
#
|
|
# smt = SmtCheckerDistribRS(drs,debug_level=3)
|
|
# smt.check_reachability(rs_examples.drs_toy_ex1_property1(),max_level=10,print_time=True)
|