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HSR + cosmetics

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Artur Meski
2016-03-03 16:11:09 +01:00
parent ec8e5d1b7d
commit 5aec7d8df5
3 changed files with 29 additions and 21 deletions
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41
rs_examples.py
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@@ -279,7 +279,7 @@ def run_counter_exp():
r.add_bg_set_entity("e")
r.add_bg_set_entity("inc")
r.add_reaction_inc("e",[("e",1),("inc",1)],[("e",N)])
r.add_reaction_inc("e","inc",[("e",1),("inc",1)],[("e",N)])
# for i in range(1,N):
# r.add_reaction([("e",i),("inc",1)],[("e",N)],[("e",i+1)])
# r.show()
@@ -289,19 +289,19 @@ def run_counter_exp():
c.add_state("working")
c.add_transition("init", [("e",1),("inc",1)], "working")
c.add_transition("working", [("inc",1)], "working")
# c.show()
# c.show()
rc = ReactionSystemWithAutomaton(r,c)
rc.show()
smt_rsc = SmtCheckerRSC(rc)
smt_rsc.check_reachability([('e',N)],print_time=True,max_level=N)
smt_rsc.check_reachability(([('e',N)],[]),print_time=True,max_level=N)
orc = rc.get_ordinary_reaction_system_with_automaton()
orc.show()
smt_tr_rs = SmtCheckerPGRS(orc)
smt_tr_rs.check_reachability(['e_' + str(N)],print_time=True)
smt_tr_rs.check_reachability(['e#' + str(N)],print_time=True)
print("Reaction System with Concentrations:", smt_rsc.get_verification_time())
print("Reaction System from translating RSC:", smt_tr_rs.get_verification_time())
@@ -352,7 +352,7 @@ def chain_reaction(print_system=False):
if verify_rsc:
smt_rsc = SmtCheckerRSC(rc)
prop = [('e_'+str(chainLen),maxConc)]
smt_rsc.check_reachability(prop,max_level=maxConc*chainLen+10)
smt_rsc.check_reachability((prop,[]),max_level=maxConc*chainLen+10)
# smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10)
else:
@@ -422,7 +422,6 @@ def blood_glucose_regulation(print_system=True):
r.add_permanency("sugar",[("expire_sugar",1)])
r.add_permanency("glycemia",[])
# moje:
r.add_reaction([("sugar",1)],[],[("sugar",1)])
@@ -447,6 +446,9 @@ def blood_glucose_regulation(print_system=True):
# smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10)
def heat_shock_response(print_system=True):
stress_temp = 42
max_temp = 50
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("hsp",1))
@@ -459,9 +461,9 @@ def heat_shock_response(print_system=True):
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",50))
stress_temp = 42
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)])
@@ -483,14 +485,22 @@ def heat_shock_response(print_system=True):
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", [("hsf",1),("prot",1),("hse",1),("temp",36)], "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",36)], "1")
c.add_transition("1", [("temp",36)], "1")
c.add_transition("1", [("temp",43)], "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("1", [("cool",1)], "1")
c.add_transition("1", [], "1")
# c.add_transition("1", [("sugar",1)], "1")
rc = ReactionSystemWithAutomaton(r,c)
@@ -500,5 +510,6 @@ def heat_shock_response(print_system=True):
smt_rsc = SmtCheckerRSC(rc)
prop = ([("hsp",1)],[("temp",stress_temp)]) # no stress
smt_rsc.check_reachability(prop,max_level=10)
#prop = ([("temp",36)],[]) # no stress
smt_rsc.check_reachability(prop,max_level=40)