From 1077dadebb12409d3b74db778f7ba929149bdb52 Mon Sep 17 00:00:00 2001 From: Artur Meski Date: Sun, 22 Sep 2019 16:40:26 +0100 Subject: [PATCH] HSR example --- smt_examples/heat_shock_response.py | 106 ++++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) create mode 100644 smt_examples/heat_shock_response.py diff --git a/smt_examples/heat_shock_response.py b/smt_examples/heat_shock_response.py new file mode 100644 index 0000000..43f5db0 --- /dev/null +++ b/smt_examples/heat_shock_response.py @@ -0,0 +1,106 @@ +#!/usr/bin/env python + +from rs import * +from smt import * +import sys +import resource + + +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 + + 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)]) + #r.add_permanency("temp",[]) + + c = ContextAutomatonWithConcentrations(r) + c.add_init_state("0") + c.add_state("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") + + 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)) + + if verify_rsc: + smt_rsc = SmtCheckerRSC(rc) + 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 = SmtCheckerRS(orc) + smt_tr_rs.check_reachability(rs_prop) + + +def main(): + + heat_shock_response() + +if __name__ == "__main__": + main() + +# EOF