from rs import * from smt import * import rs_examples from logics import * import sys import resource def run_tests(cmd_args): # test_extended_automaton() # process() # heat_shock_response() # scalable_chain(print_system=True) # example44() # example44_param() simple_param(cmd_args) def trivial_param(): r = ReactionSystemWithConcentrationsParam() r.add_bg_set_entity(("x", 3)) r.add_bg_set_entity(("c", 3)) r.add_bg_set_entity(("final", 1)) param_p1 = r.get_param("P1") r.add_reaction(param_p1, [("c", 1)], [("final", 1)]) # r.add_reaction([("x", 1)], [("c", 1)], [("final", 1)]) c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") c.add_transition("0", [("x", 1)], "1") c.add_transition("1", [], "1") rc = ReactionSystemWithAutomaton(r, c) rc.show() smt_rsc = SmtCheckerRSCParam(rc) f1 = Formula_rsLTL.f_F( BagDescription.f_TRUE(), BagDescription.f_entity("final") >= 1) # # WARNING: depth limit is set # smt_rsc.check_rsltl(formula=f1, max_level=10, print_witness=True) def simple_param(cmd_args): r = ReactionSystemWithConcentrationsParam() r.add_bg_set_entity(("x", 3)) r.add_bg_set_entity(("y", 3)) r.add_bg_set_entity(("c", 3)) r.add_bg_set_entity(("z", 3)) r.add_bg_set_entity(("final", 1)) param_p1 = r.get_param("P1") r.add_reaction([("x", 1)], [("c", 1)], [("y", 2)]) # r.add_reaction([("y", 1)], [("c", 1)], [("z", 1)]) r.add_reaction([("y", 1)], [("c", 1)], r.get_param("P2")) r.add_reaction(param_p1, [("x", 1)], [("final", 1)]) # r.add_reaction([("z", 1)], [("x", 1)], [("final", 1)]) c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") c.add_transition("0", [("x", 1)], "1") c.add_transition("1", [], "1") rc = ReactionSystemWithAutomaton(r, c) rc.show() smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise) f1 = Formula_rsLTL.f_F( BagDescription.f_TRUE(), BagDescription.f_entity("final") >= 1) # # WARNING: depth limit is set # smt_rsc.check_rsltl(formula=f1, max_level=10, print_witness=True, cont_if_sat=False) def example44_param(): r = ReactionSystemWithConcentrationsParam() r.add_bg_set_entity(("x", 2)) r.add_bg_set_entity(("y", 4)) r.add_bg_set_entity(("h", 2)) r.add_bg_set_entity(("m", 1)) r.add_reaction([("y", 1), ("x", 1)], [("y", 2), ("h", 1)], [("y", 2)]) r.add_reaction([("y", 2), ("x", 2)], [("y", 3), ("h", 1)], [("y", 3)]) r.add_reaction([("y", 3), ("h", 1)], [("y", 4), ("h", 2)], [("y", 4)]) r.add_reaction([("y", 4), ("h", 1)], [("h", 2)], [("y", 3)]) r.add_reaction([("y", 4), ("x", 2)], [("h", 1)], [("y", 2)]) r.add_reaction([("m", 1)], [("y", 3)], [("m", 1)]) c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") c.add_transition("0", [("y", 1), ("m", 1), ("x", 1)], "1") c.add_transition("1", [("x", 1)], "1") c.add_transition("1", [("x", 1), ("h", 1)], "1") c.add_transition("1", [("x", 2)], "1") c.add_transition("1", [("x", 2), ("h", 1)], "1") c.add_transition("1", [("h", 1)], "1") rc = ReactionSystemWithAutomaton(r, c) rc.show() smt_rsc = SmtCheckerRSCParam(rc) # Universal property which seems to be true: (holds also existentially) f1 = Formula_rsLTL.f_G(BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies( (BagDescription.f_entity('y') == 2), Formula_rsLTL.f_X( (BagDescription.f_entity("x") > 1), BagDescription.f_entity("y") >= 3 ) ) ) # lets see if we can find a counterexample to this property: neg_f1 = Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0, Formula_rsLTL.f_And( (BagDescription.f_entity('y') == 2), Formula_rsLTL.f_X( (BagDescription.f_entity("x") > 1), BagDescription.f_entity("y") < 3 ) ) ) # we fix the property f1 # this one holds: f2 = Formula_rsLTL.f_G( BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies( (BagDescription.f_entity('y') == 2), Formula_rsLTL.f_X( (BagDescription.f_entity("x") > 1) & (BagDescription.f_entity("h") < 1), BagDescription.f_entity("y") >= 3))) # neg_f1 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0, # Formula_rsLTL.f_And( # (BagDescription.f_entity('y') > 0), # Formula_rsLTL.f_X( # BagDescription.f_entity("x") > 0, # Formula_rsLTL.f_X( # BagDescription.f_entity("x") > 1, # BagDescription.f_entity("y") < 3 # ) # ) # ) # )) smt_rsc.check_rsltl(formula=neg_f1) def example44(): r = ReactionSystemWithConcentrations() r.add_bg_set_entity(("x", 2)) r.add_bg_set_entity(("y", 4)) r.add_bg_set_entity(("h", 2)) r.add_bg_set_entity(("m", 1)) r.add_reaction([("y", 1), ("x", 1)], [("y", 2), ("h", 1)], [("y", 2)]) r.add_reaction([("y", 2), ("x", 2)], [("y", 3), ("h", 1)], [("y", 3)]) r.add_reaction([("y", 3), ("h", 1)], [("y", 4), ("h", 2)], [("y", 4)]) r.add_reaction([("y", 4), ("h", 1)], [("h", 2)], [("y", 3)]) r.add_reaction([("y", 4), ("x", 2)], [("h", 1)], [("y", 2)]) r.add_reaction([("m", 1)], [("y", 3)], [("m", 1)]) c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") c.add_transition("0", [("y", 1), ("m", 1), ("x", 1)], "1") c.add_transition("1", [("x", 1)], "1") c.add_transition("1", [("x", 1), ("h", 1)], "1") c.add_transition("1", [("x", 2)], "1") c.add_transition("1", [("x", 2), ("h", 1)], "1") c.add_transition("1", [("h", 1)], "1") rc = ReactionSystemWithAutomaton(r, c) rc.show() smt_rsc = SmtCheckerRSC(rc) # Universal property which seems to be true: (holds also existentially) f1 = Formula_rsLTL.f_G(BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies( (BagDescription.f_entity('y') == 2), Formula_rsLTL.f_X( (BagDescription.f_entity("x") > 1), BagDescription.f_entity("y") >= 3 ) ) ) # lets see if we can find a counterexample to this property: neg_f1 = Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0, Formula_rsLTL.f_And( (BagDescription.f_entity('y') == 2), Formula_rsLTL.f_X( (BagDescription.f_entity("x") > 1), BagDescription.f_entity("y") < 3 ) ) ) # we fix the property f1 # this one holds: f2 = Formula_rsLTL.f_G( BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies( (BagDescription.f_entity('y') == 2), Formula_rsLTL.f_X( (BagDescription.f_entity("x") > 1) & (BagDescription.f_entity("h") < 1), BagDescription.f_entity("y") >= 3))) # neg_f1 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0, # Formula_rsLTL.f_And( # (BagDescription.f_entity('y') > 0), # Formula_rsLTL.f_X( # BagDescription.f_entity("x") > 0, # Formula_rsLTL.f_X( # BagDescription.f_entity("x") > 1, # BagDescription.f_entity("y") < 3 # ) # ) # ) # )) smt_rsc.check_rsltl(formula=neg_f1) 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: ") 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(1,5+1): print("formulaNumber must be in 1..5") 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(chainLen)) == maxConc) ) ) ) print(i) 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) elif formula_number == 5: f_5 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_U( BagDescription.f_entity("inc") > 0 , BagDescription.f_entity('e_1') > 0, BagDescription.f_entity('e_2') > 0 ) ) smt_rsc.check_rsltl(formula=f_5) ########################################################################### 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)