648 lines
24 KiB
Python
648 lines
24 KiB
Python
from rs import *
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from smt import *
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import rs_examples
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from logics import *
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from rsltl_shortcuts import *
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from itertools import chain, combinations
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import sys
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import resource
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def powerset(iterable,N=None):
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if N is None:
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N = len(s)
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s = list(iterable)
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return chain.from_iterable(combinations(s, r) for r in range(N+1))
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def run_tests(cmd_args):
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# test_extended_automaton()
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# process()
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# heat_shock_response()
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# scalable_chain(print_system=True)
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# example44()
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# example44_param()
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# heat_shock_response_param(cmd_args)
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# simple_param(cmd_args)
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# param_gene_expression(cmd_args)
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def param_gene_expression(cmd_args):
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"""
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Simple gene expression example with parameters
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"""
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r = ReactionSystemWithConcentrationsParam()
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r.add_bg_set_entity(("x", 1))
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r.add_bg_set_entity(("xp", 1))
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r.add_bg_set_entity(("X", 1))
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r.add_bg_set_entity(("y", 1))
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r.add_bg_set_entity(("yp", 1))
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r.add_bg_set_entity(("Y", 1))
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r.add_bg_set_entity(("h", 1))
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r.add_bg_set_entity(("Q", 1))
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all_entities = set(r.background_set)
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lda0 = r.get_param("lda0")
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lda1 = r.get_param("lda1")
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lda2 = r.get_param("lda2")
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lda3 = r.get_param("lda3")
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r.add_reaction([("x",1)],[("h",1)],[("x",1)])
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# r.add_reaction([("x",1)],[("h",1)],[("xp",1)])
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r.add_reaction(lda0, [("h",1)],[("xp",1)])
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r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)])
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r.add_reaction([("X",1),("Y",1)],[("h",1)],[("Q",1)])
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## y
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# r.add_reaction([("y",1)],[("h",1)],[("y",1)])
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# r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
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# r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
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r.add_reaction([("y",1)],[("h",1)],lda1)
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r.add_reaction(lda2,[("h",1)],[("yp",1)])
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r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3)
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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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# the experiments starts with adding x and y:
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c.add_transition("0", [("y", 1),("x",1)], "1")
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# for all the remaining steps we have empty context sequences
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c.add_transition("1", [], "1")
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c.add_transition("1", [("h", 1)], "1")
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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# f_x1 = ltl_G(True, ltl_Implies(
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# exact_state(["x"], all_entities),
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# ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
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# f_x2 = ltl_G(True, ltl_Implies(
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# exact_state(["x", "xp"], all_entities),
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# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
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# reachability
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reach_y = ltl_F(bag_entity("h") == 0, "y")
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reach_yp = ltl_F(bag_entity("h") == 0, "yp")
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reach_Y = ltl_F(bag_entity("h") == 0, "Y")
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#
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phi_r = ltl_And(reach_y, reach_yp, reach_Y)
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# rules
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phi_c1 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_entity("y") > 0,
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ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0))))
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phi_c2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_And(bag_entity("y") > 0, bag_entity("yp") > 0),
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ltl_F(True, bag_entity("Y") > 0)))
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# delayed_Y = ltl_X(True, ltl_And(bag_entity("Y") == 0, ltl_X(True, bag_entity("Y") == 0)))
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# delayed_Y = ltl_X(True, bag_entity("Y") == 0)
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delayed_Q = ltl_And(bag_entity("Q") == 0, ltl_X(True, ltl_And(bag_entity("Q") == 0, ltl_X(True, ltl_And(bag_entity("Q") == 0, ltl_F(True, bag_entity("Q") > 0))))))
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obs_1 = ltl_And(phi_r, phi_c1, phi_c2, delayed_Q)
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# Observation related to A_x:
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obs_2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_entity("x") > 0,
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ltl_X(True, bag_And(bag_entity("x") > 0, bag_entity("xp") > 0))))
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# obs_2 = ltl_And(f_y2, reach_y, reach_Y, delayed_Y, delayed_Q)
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# f_x2 = ltl_G(True, ltl_Implies(
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# exact_state(["x", "xp"], all_entities),
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# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
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#
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related_to_x = ["x", "xp", "X"]
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related_to_y = ["y", "yp", "Y"]
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params_for_x = [lda0]
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params_for_y = [lda1, lda2, lda3]
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no_x_in_y = param_True()
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for par in params_for_y:
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for ent in related_to_x:
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no_x_in_y = param_And(no_x_in_y, param_entity(par, ent) == 0)
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no_y_in_x = param_True()
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for par in params_for_x:
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for ent in related_to_y:
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no_y_in_x = param_And(no_y_in_x, param_entity(par, ent) == 0)
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# param_constr = param_And(param_entity(lda3, "Y") > 0, param_entity(lda3, "X") == 0, param_entity(lda2, "Q") == 0, param_entity(lda1, "yp") == 0, param_entity(lda1, "Y") == 0)
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param_constr = param_And(no_y_in_x, no_x_in_y)
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smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
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#
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smt_rsc.check_rsltl(
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formulae_list=[obs_1,obs_2],
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param_constr=param_constr,
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) #, max_level=4, cont_if_sat=True)
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def gene_expression_full(cmd_args):
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"""
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Simple gene expression example
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"""
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r = ReactionSystemWithConcentrationsParam()
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r.add_bg_set_entity(("x", 1))
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r.add_bg_set_entity(("xp", 1))
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r.add_bg_set_entity(("X", 1))
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r.add_bg_set_entity(("y", 1))
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r.add_bg_set_entity(("yp", 1))
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r.add_bg_set_entity(("Y", 1))
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r.add_bg_set_entity(("z", 1))
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r.add_bg_set_entity(("zp", 1))
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r.add_bg_set_entity(("Z", 1))
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r.add_bg_set_entity(("h", 1))
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r.add_bg_set_entity(("Q", 1))
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r.add_bg_set_entity(("U", 1))
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all_entities = set(r.background_set)
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r.add_reaction([("x",1)],[("h",1)],[("x",1)])
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r.add_reaction([("x",1)],[("h",1)],[("xp",1)])
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r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)])
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## y
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# r.add_reaction([("y",1)],[("h",1)],[("y",1)])
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# r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
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# r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
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lda1 = r.get_param("lda1")
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lda2 = r.get_param("lda2")
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lda3 = r.get_param("lda3")
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r.add_reaction([("y",1)],[("h",1)],lda1)
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r.add_reaction(lda2,[("Q",1)],[("yp",1)])
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r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3)
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r.add_reaction([("z",1)],[("h",1)],[("z",1)])
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r.add_reaction([("z",1)], [("X",1)], [("zp",1)])
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r.add_reaction([("z",1),("zp",1)],[("h",1)],[("Z",1)])
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r.add_reaction([("U",1),("X",1)],[("h",1)],[("Q",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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# the experiments starts with adding x and y:
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c.add_transition("0", [("x", 1),("y", 1)], "1")
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# for all the remaining steps we have empty context sequences
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c.add_transition("1", [], "1")
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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# f_x1 = ltl_G(True, ltl_Implies(
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# exact_state(["x"], all_entities),
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# ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
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# f_x2 = ltl_G(True, ltl_Implies(
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# exact_state(["x", "xp"], all_entities),
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# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
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reach_yp = ltl_F(True, "yp")
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reach_Y = ltl_F(True, "Y")
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reach_y = ltl_F(True, "y")
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f_y1 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_And(bag_entity("Q") == 0, bag_entity("y") > 0),
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ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0))))
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f_y2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
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bag_And(bag_entity("y") > 0, bag_entity("yp") > 0),
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ltl_F(True, bag_entity("Y") > 0)))
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obs_1 = ltl_And(f_y1, reach_y)
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obs_2 = ltl_And(f_y2, reach_y, reach_Y)
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# f_x2 = ltl_G(True, ltl_Implies(
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# exact_state(["x", "xp"], all_entities),
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# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
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#
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smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
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#
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smt_rsc.check_rsltl(formulae_list=[obs_1, obs_2], max_level=3, cont_if_sat=True)
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# smt_rsc.check_rsltl(formula=f_x1, print_witness=True)
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def trivial_param():
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r = ReactionSystemWithConcentrationsParam()
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r.add_bg_set_entity(("x", 3))
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r.add_bg_set_entity(("c", 3))
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r.add_bg_set_entity(("final", 1))
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param_p1 = r.get_param("P1")
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r.add_reaction(param_p1, [("c", 1)], [("final", 1)])
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# r.add_reaction([("x", 1)], [("c", 1)], [("final", 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", [("x", 1)], "1")
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c.add_transition("1", [], "1")
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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smt_rsc = SmtCheckerRSCParam(rc)
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f1 = ltl_F(True, bag_entity("final") >= 1)
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# f1 = Formula_rsLTL.f_F(
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# BagDescription.f_TRUE(),
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# BagDescription.f_entity("final") >= 1)
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#
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# WARNING: depth limit is set
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#
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smt_rsc.check_rsltl(formula=f1, max_level=10, print_witness=True)
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def simple_param(cmd_args):
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r = ReactionSystemWithConcentrationsParam()
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r.add_bg_set_entity(("x", 3))
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r.add_bg_set_entity(("y", 3))
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r.add_bg_set_entity(("c", 3))
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r.add_bg_set_entity(("z", 3))
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r.add_bg_set_entity(("final", 1))
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param_p1 = r.get_param("P1")
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r.add_reaction([("x", 1)], [("c", 1)], [("y", 2)])
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# r.add_reaction([("y", 1)], [("c", 1)], [("z", 1)])
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r.add_reaction([("y", 1)], [("c", 1)], r.get_param("P2"))
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r.add_reaction(param_p1, [("x", 1)], [("final", 1)])
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# r.add_reaction([("z", 1)], [("x", 1)], [("final", 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", [("x", 1)], "1")
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c.add_transition("1", [], "1")
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
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f1 = Formula_rsLTL.f_F(
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BagDescription.f_TRUE(),
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BagDescription.f_entity("final") >= 1)
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#
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# WARNING: depth limit is set
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#
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smt_rsc.check_rsltl(formula=f1, max_level=10, print_witness=True, cont_if_sat=False)
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def heat_shock_response_param(cmd_args, print_system=True):
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stress_temp = 42
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max_temp = 50
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r = ReactionSystemWithConcentrationsParam()
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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(("stress",1))
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r.add_bg_set_entity(("no_stress",1))
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param_p1 = r.get_param("P1")
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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),("stress",1)],[], [("hsf",1),("hsp",1)])
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r.add_reaction([("hsp:hsf",1)], [("stress",1)],[("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([("stress",1),("prot",1)], [], [("mfp",1),("prot",1)])
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r.add_reaction([("prot",1)], [("stress",1)], [("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),("no_stress",1)], "1")
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c.add_transition("1", [("stress",1)], "1")
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c.add_transition("1", [("no_stress",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 = [("hsp:hsf",1),("hse",1),("prot",1)]
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# prop_block = [("temp",stress_temp)]
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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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#
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# f_reach_mfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("mfp") > 0) )
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f_reach_mfp = ltl_F(True, bag_entity("mfp") > 0)
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f_reach_hspmfp = Formula_rsLTL.f_F(BagDescription.f_TRUE(), (BagDescription.f_entity("hsp:mfp") > 0) )
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smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
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smt_rsc.check_rsltl(formulae_list=[f_reach_mfp, f_reach_hspmfp])
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# (1) if we keep increasing the temperature the protein will eventually misfold
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# f_mfp_when_heating = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
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# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("mfp") > 0) )
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# )
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# smt_rsc.check_rsltl(formula=f_mfp_when_heating)
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|
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# (2) when heating, we finally exceed the stress_temp
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# f_2 = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
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# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("temp") > stress_temp))
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# )
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# smt_rsc.check_rsltl(formula=f_2)
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# smt_rsc.check_reachability(prop,max_level=40)
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def example44_param():
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|
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r = ReactionSystemWithConcentrationsParam()
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r.add_bg_set_entity(("x", 2))
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r.add_bg_set_entity(("y", 4))
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r.add_bg_set_entity(("h", 2))
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r.add_bg_set_entity(("m", 1))
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|
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r.add_reaction([("y", 1), ("x", 1)], [("y", 2), ("h", 1)], [("y", 2)])
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r.add_reaction([("y", 2), ("x", 2)], [("y", 3), ("h", 1)], [("y", 3)])
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r.add_reaction([("y", 3), ("h", 1)], [("y", 4), ("h", 2)], [("y", 4)])
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r.add_reaction([("y", 4), ("h", 1)], [("h", 2)], [("y", 3)])
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r.add_reaction([("y", 4), ("x", 2)], [("h", 1)], [("y", 2)])
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r.add_reaction([("m", 1)], [("y", 3)], [("m", 1)])
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|
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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", [("y", 1), ("m", 1), ("x", 1)], "1")
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c.add_transition("1", [("x", 1)], "1")
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c.add_transition("1", [("x", 1), ("h", 1)], "1")
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c.add_transition("1", [("x", 2)], "1")
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c.add_transition("1", [("x", 2), ("h", 1)], "1")
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c.add_transition("1", [("h", 1)], "1")
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|
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rc = ReactionSystemWithAutomaton(r, c)
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rc.show()
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smt_rsc = SmtCheckerRSCParam(rc)
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|
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# Universal property which seems to be true: (holds also existentially)
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f1 = Formula_rsLTL.f_G(BagDescription.f_entity("x") > 0,
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Formula_rsLTL.f_Implies(
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|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
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|
BagDescription.f_entity("y") >= 3
|
|
)
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|
)
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)
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|
|
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# lets see if we can find a counterexample to this property:
|
|
neg_f1 = Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
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Formula_rsLTL.f_And(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") < 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# we fix the property f1
|
|
# this one holds:
|
|
f2 = Formula_rsLTL.f_G(
|
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BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1) &
|
|
(BagDescription.f_entity("h") < 1),
|
|
BagDescription.f_entity("y") >= 3)))
|
|
|
|
# neg_f1 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_And(
|
|
# (BagDescription.f_entity('y') > 0),
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 1,
|
|
# BagDescription.f_entity("y") < 3
|
|
# )
|
|
# )
|
|
# )
|
|
# ))
|
|
smt_rsc.check_rsltl(formula=neg_f1)
|
|
|
|
|
|
def example44():
|
|
|
|
r = ReactionSystemWithConcentrations()
|
|
r.add_bg_set_entity(("x", 2))
|
|
r.add_bg_set_entity(("y", 4))
|
|
r.add_bg_set_entity(("h", 2))
|
|
r.add_bg_set_entity(("m", 1))
|
|
|
|
r.add_reaction([("y", 1), ("x", 1)], [("y", 2), ("h", 1)], [("y", 2)])
|
|
r.add_reaction([("y", 2), ("x", 2)], [("y", 3), ("h", 1)], [("y", 3)])
|
|
r.add_reaction([("y", 3), ("h", 1)], [("y", 4), ("h", 2)], [("y", 4)])
|
|
r.add_reaction([("y", 4), ("h", 1)], [("h", 2)], [("y", 3)])
|
|
r.add_reaction([("y", 4), ("x", 2)], [("h", 1)], [("y", 2)])
|
|
r.add_reaction([("m", 1)], [("y", 3)], [("m", 1)])
|
|
|
|
c = ContextAutomatonWithConcentrations(r)
|
|
c.add_init_state("0")
|
|
c.add_state("1")
|
|
c.add_transition("0", [("y", 1), ("m", 1), ("x", 1)], "1")
|
|
c.add_transition("1", [("x", 1)], "1")
|
|
c.add_transition("1", [("x", 1), ("h", 1)], "1")
|
|
c.add_transition("1", [("x", 2)], "1")
|
|
c.add_transition("1", [("x", 2), ("h", 1)], "1")
|
|
c.add_transition("1", [("h", 1)], "1")
|
|
|
|
rc = ReactionSystemWithAutomaton(r, c)
|
|
rc.show()
|
|
smt_rsc = SmtCheckerRSC(rc)
|
|
|
|
# Universal property which seems to be true: (holds also existentially)
|
|
f1 = Formula_rsLTL.f_G(BagDescription.f_entity("x") > 0,
|
|
Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") >= 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# lets see if we can find a counterexample to this property:
|
|
neg_f1 = Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
Formula_rsLTL.f_And(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1),
|
|
BagDescription.f_entity("y") < 3
|
|
)
|
|
)
|
|
)
|
|
|
|
# we fix the property f1
|
|
# this one holds:
|
|
f2 = Formula_rsLTL.f_G(
|
|
BagDescription.f_entity("x") > 0, Formula_rsLTL.f_Implies(
|
|
(BagDescription.f_entity('y') == 2),
|
|
Formula_rsLTL.f_X(
|
|
(BagDescription.f_entity("x") > 1) &
|
|
(BagDescription.f_entity("h") < 1),
|
|
BagDescription.f_entity("y") >= 3)))
|
|
|
|
# neg_f1 = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_F(BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_And(
|
|
# (BagDescription.f_entity('y') > 0),
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 0,
|
|
# Formula_rsLTL.f_X(
|
|
# BagDescription.f_entity("x") > 1,
|
|
# BagDescription.f_entity("y") < 3
|
|
# )
|
|
# )
|
|
# )
|
|
# ))
|
|
smt_rsc.check_rsltl(formula=neg_f1)
|
|
|
|
|
|
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)
|
|
|
|
# (1) if we keep increasing the temperature the protein will eventually misfold
|
|
# f_mfp_when_heating = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
# Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("mfp") > 0) )
|
|
# )
|
|
# smt_rsc.check_rsltl(formula=f_mfp_when_heating)
|
|
|
|
# (2) when heating, we finally exceed the stress_temp
|
|
f_2 = Formula_rsLTL.f_X(BagDescription.f_TRUE(),
|
|
Formula_rsLTL.f_F(BagDescription.f_entity("heat") > 0, (BagDescription.f_entity("temp") > stress_temp))
|
|
)
|
|
smt_rsc.check_rsltl(formula=f_2)
|
|
|
|
# smt_rsc.check_reachability(prop,max_level=40)
|
|
|
|
def state_translate_rsc2rs(p):
|
|
return [e[0] + "#" + str(e[1]) for e in p]
|
|
|