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Cleanup, example

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Artur Meski
2017-12-27 21:35:39 +00:00
parent efa4767394
commit 8d89047941
3 changed files with 260 additions and 134 deletions
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138
rs_testing.py
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@@ -26,6 +26,80 @@ def gene_expression(cmd_args):
"""
r = ReactionSystemWithConcentrationsParam()
r.add_bg_set_entity(("y", 1))
r.add_bg_set_entity(("yp", 1))
r.add_bg_set_entity(("Y", 1))
r.add_bg_set_entity(("h", 1))
all_entities = set(r.background_set)
## y
# r.add_reaction([("y",1)],[("h",1)],[("y",1)])
# r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
# r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
lda1 = r.get_param("lda1")
lda2 = r.get_param("lda2")
lda3 = r.get_param("lda3")
r.add_reaction([("y",1)],[("h",1)],lda1)
r.add_reaction(lda2,[("h",1)],[("yp",1)])
r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3)
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("0")
c.add_state("1")
# the experiments starts with adding x and y:
c.add_transition("0", [("y", 1)], "1")
# for all the remaining steps we have empty context sequences
c.add_transition("1", [], "1")
rc = ReactionSystemWithAutomaton(r, c)
rc.show()
# f_x1 = ltl_G(True, ltl_Implies(
# exact_state(["x"], all_entities),
# ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
# f_x2 = ltl_G(True, ltl_Implies(
# exact_state(["x", "xp"], all_entities),
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
reach_yp = ltl_F(True, "yp")
reach_Y = ltl_F(True, "Y")
reach_y = ltl_F(True, "y")
f_y1 = ltl_G(bag_entity("h") == 0, ltl_Implies(
bag_entity("y") > 0,
ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0))))
f_y2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
bag_And(bag_entity("y") > 0, bag_entity("yp") > 0),
ltl_F(True, bag_entity("Y") > 0)))
# delayed_Y = ltl_X(True, ltl_And(bag_entity("Y") == 0, ltl_X(True, bag_entity("Y") == 0)))
delayed_Y = ltl_X(True, bag_entity("Y") == 0)
obs_1 = ltl_And(f_y1, reach_y, delayed_Y)
obs_2 = ltl_And(f_y2, reach_y, reach_Y, delayed_Y)
# f_x2 = ltl_G(True, ltl_Implies(
# exact_state(["x", "xp"], all_entities),
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
#
smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
#
smt_rsc.check_rsltl(formulae_list=[obs_1, obs_2], max_level=4, cont_if_sat=True)
# smt_rsc.check_rsltl(formula=f_x1, print_witness=True)
def gene_expression_full(cmd_args):
"""
Simple gene expression example
"""
r = ReactionSystemWithConcentrationsParam()
r.add_bg_set_entity(("x", 1))
r.add_bg_set_entity(("xp", 1))
r.add_bg_set_entity(("X", 1))
@@ -45,23 +119,24 @@ def gene_expression(cmd_args):
all_entities = set(r.background_set)
r.add_reaction([("x",1)],[("h",1)],[("x",1)])
r.add_reaction([("x",1)],[("h",1)],[("xp",1)])
r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)])
# r.add_reaction([("x",1)],[("h",1)],[("xp",1)])
param_p1 = r.get_param("P1")
r.add_reaction(param_p1,[("h",1)],[("xp",1)])
# r.add_reaction([("x",1),("xp",1)],[("h",1)],[("X",1)])
param_p2_r = r.get_param("P2_r")
param_p2_i = r.get_param("P2_i")
param_p2_p = r.get_param("P2_p")
r.add_reaction(param_p2_r,param_p2_i,param_p2_p)
## y
# r.add_reaction([("y",1)],[("h",1)],[("y",1)])
# r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
# r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
lda1 = r.get_param("lda1")
lda2 = r.get_param("lda2")
lda3 = r.get_param("lda3")
r.add_reaction([("y",1)],[("h",1)],lda1)
r.add_reaction(lda2,[("Q",1)],[("yp",1)])
r.add_reaction([("y",1),("yp",1)],[("h",1)],lda3)
r.add_reaction([("y",1)],[("h",1)],[("y",1)])
r.add_reaction([("y",1)],[("Q",1)],[("yp",1)])
r.add_reaction([("y",1),("yp",1)],[("h",1)],[("Y",1)])
r.add_reaction([("z",1)],[("h",1)],[("z",1)])
r.add_reaction([("z",1)], [("X",1)], [("zp",1)])
r.add_reaction([("z",1),("zp",1)],[("h",1)],[("Z",1)])
r.add_reaction([("U",1),("X",1)],[("h",1)],[("Q",1)])
c = ContextAutomatonWithConcentrations(r)
@@ -77,19 +152,36 @@ def gene_expression(cmd_args):
rc = ReactionSystemWithAutomaton(r, c)
rc.show()
f_x1 = ltl_G(True, ltl_Implies(
exact_state(["x"], all_entities),
ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
f_x2 = ltl_G(True, ltl_Implies(
exact_state(["x", "xp"], all_entities),
ltl_X(bag_Not("h"), exact_state("X", all_entities))))
reach_xp = ltl_F(True, "xp")
reach_X = ltl_F(True, "X")
# f_x1 = ltl_G(True, ltl_Implies(
# exact_state(["x"], all_entities),
# ltl_X(bag_And(bag_Not("Y"), bag_Not("Z"), bag_Not("h")), exact_state(["x", "xp"], all_entities))))
# f_x2 = ltl_G(True, ltl_Implies(
# exact_state(["x", "xp"], all_entities),
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
reach_yp = ltl_F(True, "yp")
reach_Y = ltl_F(True, "Y")
reach_y = ltl_F(True, "y")
f_y1 = ltl_G(bag_entity("h") == 0, ltl_Implies(
bag_And(bag_entity("Q") == 0, bag_entity("y") > 0),
ltl_X(True, bag_And(bag_entity("y") > 0, bag_entity("yp") > 0))))
f_y2 = ltl_G(bag_entity("h") == 0, ltl_Implies(
bag_And(bag_entity("y") > 0, bag_entity("yp") > 0),
ltl_F(True, bag_entity("Y") > 0)))
obs_1 = ltl_And(f_y1, reach_y)
obs_2 = ltl_And(f_y2, reach_y, reach_Y)
# f_x2 = ltl_G(True, ltl_Implies(
# exact_state(["x", "xp"], all_entities),
# ltl_X(bag_Not("h"), exact_state("X", all_entities))))
#
smt_rsc = SmtCheckerRSCParam(rc, optimise=cmd_args.optimise)
smt_rsc.check_rsltl(formulae_list=[f_x1, f_x2, reach_xp, reach_X])
#
smt_rsc.check_rsltl(formulae_list=[obs_1, obs_2], max_level=3, cont_if_sat=True)
# smt_rsc.check_rsltl(formula=f_x1, print_witness=True)