af26ca543b
- 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
134 lines
4.8 KiB
Python
Executable File
134 lines
4.8 KiB
Python
Executable File
#!/usr/bin/env python
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#
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# Copyright (c) 2015-2019 Artur Meski
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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# in the Software without restriction, including without limitation the rights
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# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# copies of the Software, and to permit persons to whom the Software is
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# furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included in all
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# copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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#
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from rs import *
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from smt import *
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import sys
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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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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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print(" - 0 -- RSC translated into RS")
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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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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(
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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("1", [], "1")
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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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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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else:
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orc = rc.get_ordinary_reaction_system_with_automaton()
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if print_system:
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print("\nTranslated:")
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orc.show()
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smt_tr_rs = SmtCheckerRS(orc)
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smt_tr_rs.check_reachability(rs_prop)
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def state_translate_rsc2rs(p):
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return [e[0] + "#" + str(e[1]) for e in 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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