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preparing for experiments, HSR -- reachability testing via rsLTL; some cleanup

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Artur Meski
2017-03-12 15:29:28 +01:00
parent 5934c6381d
commit 05557440a0
3 changed files with 92 additions and 6 deletions
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83
rs_testing.py
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@@ -2,17 +2,94 @@ from rs import *
from smt import *
import rs_examples
from logics import *
import sys
import resource
def run_tests():
# test_extended_automaton()
# process()
test_rsLTL()
heat_shock_response()
def heat_shock_response(print_system=True):
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)])
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("0")
c.add_state("1")
c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1")
c.add_transition("1", [("cool",1)], "1")
c.add_transition("1", [("heat",1)], "1")
c.add_transition("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))
f_reach_mfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("mfp") > 0) )
smt_rsc = SmtCheckerRSC(rc)
# smt_rsc.check_reachability(prop,max_level=40)
smt_rsc.check_rsltl(formula=f_reach_mfp)
def state_translate_rsc2rs(p):
return [e[0] + "#" + str(e[1]) for e in p]
def test_rsLTL():
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("inc",2))
r.add_bg_set_entity(("ent1",1))
r.add_bg_set_entity(("ent2",5))
r.add_reaction([("ent2",1),("inc",1)],[],[("ent2",2)])
r.add_reaction([("ent2",2)],[],[("ent2",2)])
@@ -24,9 +101,9 @@ def test_rsLTL():
c.add_transition("working", [("inc",1)], "working")
# x = ( Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_bag( ~((BagDescription.f_entity("ent1") == 3) | (BagDescription.f_entity("ent2") < 3)) ) ) ) & Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_bag( ~((BagDescription.f_entity("ent3") == 1) ) ) )
# x = Formula_rsLTL.f_G((BagDescription.f_entity("inc") > 0), (BagDescription.f_entity("ent1") == 3) | (BagDescription.f_entity("ent2") < 3))
x = Formula_rsLTL.f_G((BagDescription.f_entity("inc") > 0), (BagDescription.f_entity("ent1") == 3) | (BagDescription.f_entity("ent2") < 3))
x = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("ent2") == 2) )
#x = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("ent2") == 2) )
print(x)