Examples and clean-ups (#1)
- Attempt at implementing an example for DRS - Complete reactions set - New automaton - Formula - Fixed automaton scaling - Proc index in the formula - Benchmark generators - Scripts to reproduce experiments for reaction mining
This commit was merged in pull request #1.
This commit is contained in:
Artur Meski
117
examples/smt/heat_shock_response.py
Normal file → Executable file
117
examples/smt/heat_shock_response.py
Normal file → Executable file
@@ -28,8 +28,7 @@ import resource
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def heat_shock_response(print_system=True, verify_rsc=True):
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if len(sys.argv) < 1+1:
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if len(sys.argv) < 1 + 1:
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print("{source} <type>".format(source=sys.argv[0]))
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print("type:")
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print(" - 1 -- RSC")
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@@ -37,72 +36,80 @@ def heat_shock_response(print_system=True, verify_rsc=True):
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print()
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exit(1)
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verify_rsc=bool(int(sys.argv[1]))
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verify_rsc = bool(int(sys.argv[1]))
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stress_temp = 42
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max_temp = 50
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity(("hsp",1))
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r.add_bg_set_entity(("hsf",1))
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r.add_bg_set_entity(("hsf2",1))
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r.add_bg_set_entity(("hsf3",1))
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r.add_bg_set_entity(("hse",1))
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r.add_bg_set_entity(("mfp",1))
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r.add_bg_set_entity(("prot",1))
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r.add_bg_set_entity(("hsf3:hse",1))
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r.add_bg_set_entity(("hsp:mfp",1))
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r.add_bg_set_entity(("hsp:hsf",1))
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r.add_bg_set_entity(("temp",max_temp))
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r.add_bg_set_entity(("heat",1))
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r.add_bg_set_entity(("cool",1))
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r.add_reaction([("hsf",1)], [("hsp",1)], [("hsf3",1)])
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r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)])
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r.add_reaction([("hsf3",1)], [("hse",1),("hsp",1)],[("hsf",1)])
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r.add_reaction([("hsf3",1),("hsp",1),("mfp",1)], [("hse",1)], [("hsf",1)])
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r.add_reaction([("hsf3",1),("hse",1)], [("hsp",1)], [("hsf3:hse",1)])
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r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[], [("hsf3:hse",1)])
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r.add_reaction([("hse",1)], [("hsf3",1)], [("hse",1)])
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r.add_reaction([("hsp",1),("hsf3",1),("hse",1)], [("mfp",1)], [("hse",1)])
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r.add_reaction([("hsf3:hse",1)], [("hsp",1)], [("hsp",1),("hsf3:hse",1)])
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r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[], [("hsp",1),("hsf3:hse",1)])
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r.add_reaction([("hsf",1),("hsp",1)], [("mfp",1)], [("hsp:hsf",1)])
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r.add_reaction([("hsp:hsf",1),("temp",stress_temp)],[], [("hsf",1),("hsp",1)])
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r.add_reaction([("hsp:hsf",1)], [("temp",stress_temp)],[("hsp:hsf",1)])
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r.add_reaction([("hsp",1),("hsf3:hse",1)], [("mfp",1)], [("hse",1),("hsp:hsf",1)])
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r.add_reaction([("temp",stress_temp),("prot",1)], [], [("mfp",1),("prot",1)])
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r.add_reaction([("prot",1)], [("temp",stress_temp)], [("prot",1)])
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r.add_reaction([("hsp",1),("mfp",1)], [], [("hsp:mfp",1)])
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r.add_reaction([("mfp",1)], [("hsp",1)], [("mfp",1)])
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r.add_reaction([("hsp:mfp",1)], [], [("hsp",1),("prot",1)])
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r.add_reaction_inc("temp", "heat", [("temp",1)],[("temp",max_temp)])
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r.add_reaction_dec("temp", "cool", [("temp",1)],[])
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity(("hsp", 1))
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r.add_bg_set_entity(("hsf", 1))
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r.add_bg_set_entity(("hsf2", 1))
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r.add_bg_set_entity(("hsf3", 1))
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r.add_bg_set_entity(("hse", 1))
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r.add_bg_set_entity(("mfp", 1))
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r.add_bg_set_entity(("prot", 1))
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r.add_bg_set_entity(("hsf3:hse", 1))
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r.add_bg_set_entity(("hsp:mfp", 1))
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r.add_bg_set_entity(("hsp:hsf", 1))
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r.add_bg_set_entity(("temp", max_temp))
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r.add_bg_set_entity(("heat", 1))
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r.add_bg_set_entity(("cool", 1))
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r.add_permanency("temp",[("heat",1),("cool",1)])
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r.add_reaction([("hsf", 1)], [("hsp", 1)], [("hsf3", 1)])
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r.add_reaction([("hsf", 1), ("hsp", 1), ("mfp", 1)], [], [("hsf3", 1)])
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r.add_reaction([("hsf3", 1)], [("hse", 1), ("hsp", 1)], [("hsf", 1)])
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r.add_reaction([("hsf3", 1), ("hsp", 1), ("mfp", 1)], [("hse", 1)], [("hsf", 1)])
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r.add_reaction([("hsf3", 1), ("hse", 1)], [("hsp", 1)], [("hsf3:hse", 1)])
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r.add_reaction(
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[("hsp", 1), ("hsf3", 1), ("mfp", 1), ("hse", 1)], [], [("hsf3:hse", 1)]
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)
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r.add_reaction([("hse", 1)], [("hsf3", 1)], [("hse", 1)])
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r.add_reaction([("hsp", 1), ("hsf3", 1), ("hse", 1)], [("mfp", 1)], [("hse", 1)])
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r.add_reaction([("hsf3:hse", 1)], [("hsp", 1)], [("hsp", 1), ("hsf3:hse", 1)])
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r.add_reaction(
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[("hsp", 1), ("mfp", 1), ("hsf3:hse", 1)], [], [("hsp", 1), ("hsf3:hse", 1)]
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)
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r.add_reaction([("hsf", 1), ("hsp", 1)], [("mfp", 1)], [("hsp:hsf", 1)])
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r.add_reaction(
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[("hsp:hsf", 1), ("temp", stress_temp)], [], [("hsf", 1), ("hsp", 1)]
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)
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r.add_reaction([("hsp:hsf", 1)], [("temp", stress_temp)], [("hsp:hsf", 1)])
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r.add_reaction(
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[("hsp", 1), ("hsf3:hse", 1)], [("mfp", 1)], [("hse", 1), ("hsp:hsf", 1)]
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)
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r.add_reaction([("temp", stress_temp), ("prot", 1)], [], [("mfp", 1), ("prot", 1)])
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r.add_reaction([("prot", 1)], [("temp", stress_temp)], [("prot", 1)])
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r.add_reaction([("hsp", 1), ("mfp", 1)], [], [("hsp:mfp", 1)])
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r.add_reaction([("mfp", 1)], [("hsp", 1)], [("mfp", 1)])
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r.add_reaction([("hsp:mfp", 1)], [], [("hsp", 1), ("prot", 1)])
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r.add_reaction_inc("temp", "heat", [("temp", 1)], [("temp", max_temp)])
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r.add_reaction_dec("temp", "cool", [("temp", 1)], [])
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r.add_permanency("temp", [("heat", 1), ("cool", 1)])
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c = ContextAutomatonWithConcentrations(r)
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c.add_init_state("0")
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c.add_state("1")
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c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1")
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c.add_transition("1", [("cool",1)], "1")
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c.add_transition("1", [("heat",1)], "1")
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c.add_transition("0", [("hsf", 1), ("prot", 1), ("hse", 1), ("temp", 35)], "1")
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c.add_transition("1", [("cool", 1)], "1")
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c.add_transition("1", [("heat", 1)], "1")
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c.add_transition("1", [], "1")
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rc = ReactionSystemWithAutomaton(r,c)
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rc = ReactionSystemWithAutomaton(r, c)
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if print_system:
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rc.show()
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prop_req = [ ("mfp",1) ]
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prop_block = [ ]
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prop = (prop_req,prop_block)
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rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
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prop_req = [("mfp", 1)]
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prop_block = []
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prop = (prop_req, prop_block)
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rs_prop = (state_translate_rsc2rs(prop_req), state_translate_rsc2rs(prop_block))
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if verify_rsc:
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smt_rsc = SmtCheckerRSC(rc)
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smt_rsc.check_reachability(prop,max_level=40)
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smt_rsc.check_reachability(prop, max_level=40)
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else:
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orc = rc.get_ordinary_reaction_system_with_automaton()
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if print_system:
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@@ -117,10 +124,10 @@ def state_translate_rsc2rs(p):
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def main():
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heat_shock_response()
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if __name__ == "__main__":
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main()
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# EOF
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