From 9f3af0b48cbf227ecff06b9a0c898a4d0964bade Mon Sep 17 00:00:00 2001 From: Artur Meski Date: Fri, 4 Mar 2016 23:50:38 +0100 Subject: [PATCH] HSR. Translation of properties RSC->RS. Testing with RS and RSC (cmdline args). --- rs_examples.py | 82 ++++++++++++++++++++++++++++++++------------------ 1 file changed, 53 insertions(+), 29 deletions(-) diff --git a/rs_examples.py b/rs_examples.py index e641c2d..1da79c2 100755 --- a/rs_examples.py +++ b/rs_examples.py @@ -445,7 +445,15 @@ def blood_glucose_regulation(print_system=True): smt_rsc.check_reachability(prop,max_level=10) # smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10) -def heat_shock_response(print_system=True): +def heat_shock_response(print_system=True,verify_rsc=True): + + if len(sys.argv) < 1+1: + print("provide B") + print(" B=1 - RSC") + print(" B=0 - Translated RSC into RS") + exit(1) + + verify_rsc=bool(int(sys.argv[1])) stress_temp = 42 max_temp = 50 @@ -465,25 +473,25 @@ def heat_shock_response(print_system=True): 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)],[("hsp",1),("hse",1)],[("hsf",1)]) - r.add_reaction([("hsp",1),("hsf3",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)],[("mfp",1),("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([("hsf",1)], [("hsp",1)], [("hsf3",1)]) + r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)]) + r.add_reaction([("hsf3",1)], [("hsp",1),("hse",1)],[("hsf",1)]) + r.add_reaction([("hsp",1),("hsf3",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)],[("mfp",1),("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)],[]) @@ -494,12 +502,12 @@ def heat_shock_response(print_system=True): c = ContextAutomatonWithConcentrations(r) c.add_init_state("0") c.add_state("1") - c.add_transition("0", [("temp",20)], "1") - c.add_transition("1", [("hsf",1),("prot",1),("hse",1),("temp",20)], "1") - #c.add_transition("1", [("hse",1),("prot",1),("hsp:hsf",1),("temp",stress_temp)], "1") - c.add_transition("1", [("hsp",1),("prot",1),("hsf3:hse",1),("mfp",1),("hsp:mfp",1),("temp",20)], "1") - c.add_transition("1", [("heat",1)], "1") + # c.add_transition("0", [("prot",1), ("temp",35)], "1") + c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1") + c.add_transition("0", [("hse",1),("prot",1),("hsp:hsf",1),("temp",stress_temp)], "1") + # c.add_transition("0", [("hsp",1),("prot",1),("hsf3:hse",1),("mfp",1),("hsp:mfp",1),("temp",30)], "1") c.add_transition("1", [("cool",1)], "1") + c.add_transition("1", [("heat",1)], "1") c.add_transition("1", [], "1") # c.add_transition("1", [("sugar",1)], "1") @@ -508,8 +516,24 @@ def heat_shock_response(print_system=True): if print_system: rc.show() - smt_rsc = SmtCheckerRSC(rc) - prop = ([("hsp",1)],[("temp",stress_temp)]) # no stress - #prop = ([("temp",36)],[]) # no stress - smt_rsc.check_reachability(prop,max_level=40) + prop_req = [("hsp",1),("prot",1),("hsf3:hse",1),("mfp",1),("hsp:mfp",1),("temp",30)] + prop_block = [("temp",stress_temp)] + prop = (prop_req,prop_block) + rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block)) + + if verify_rsc: + smt_rsc = SmtCheckerRSC(rc) + # prop = ([("mfp",1)],[("temp",21)]) # no stress + #prop = ([("temp",36)],[]) # no stress + smt_rsc.check_reachability(prop,max_level=40) + else: + orc = rc.get_ordinary_reaction_system_with_automaton() + if print_system: + print("\nTranslated:") + orc.show() + smt_tr_rs = SmtCheckerPGRS(orc) + smt_tr_rs.check_reachability(rs_prop) +def state_translate_rsc2rs(p): + return [e[0] + "#" + str(e[1]) for e in p] +