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HSR example

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Artur Meski
2019-09-22 16:40:26 +01:00
parent dc6213743e
commit 1077dadebb
1 changed files with 106 additions and 0 deletions
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smt_examples/heat_shock_response.py Normal file
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#!/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