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HSR. Translation of properties RSC->RS. Testing with RS and RSC (cmdline args).

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This commit is contained in:
Artur Meski
2016-03-04 23:50:38 +01:00
parent ef1b769654
commit 9f3af0b48c
1 changed files with 53 additions and 29 deletions
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82
rs_examples.py
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@@ -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]