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introducing parameters

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This commit is contained in:
Artur Meski
2017-09-03 17:59:26 +01:00
parent 2957a7ac52
commit 782ae117a3
4 changed files with 75 additions and 43 deletions
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4
rs/__init__.py
View File

@@ -2,11 +2,11 @@ from rs.reaction_system import ReactionSystem
from rs.context_automaton import ContextAutomaton
from rs.reaction_system_with_concentrations import ReactionSystemWithConcentrations
from rs.reaction_system_with_concentrations_param import ReactionSystemWithConcentrationsParam
from rs.reaction_system_with_concentrations_param import ReactionSystemWithConcentrationsParam, ParameterObj
from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
from rs.extended_context_automaton import ExtendedContextAutomaton
from rs.network_of_context_automata import NetworkOfContextAutomata
from rs.reaction_system_with_automaton import ReactionSystemWithAutomaton
from rs.reaction_system_with_autnet import ReactionSystemWithNetworkOfAutomata
from rs.reaction_system_with_autnet import ReactionSystemWithNetworkOfAutomata

90
rs/reaction_system_with_concentrations_param.py
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@@ -3,10 +3,13 @@ from colour import *
from rs.reaction_system import ReactionSystem
class ParameterSet(object):
class ParameterObj(object):
def __init__(self, name):
self.name = name
def __repr__(self):
return "@{0}".format(self.name)
class ReactionSystemWithConcentrationsParam(ReactionSystem):
@@ -14,6 +17,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def __init__(self):
self.reactions = []
self.parametric_reactions = []
self.meta_reactions = dict()
self.permanent_entities = dict()
self.background_set = []
@@ -85,31 +89,55 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
if R == [] and not ignore_empty_R:
raise RuntimeError("No reactants defined")
#
# REACTANTS
#
reactants = []
for r in R:
self.is_valid_entity_with_concentration(r)
self.has_non_zero_concentration(r)
entity, level = r
reactants.append((self.get_entity_id(entity), level))
if self.max_concentration < level:
self.max_concentration = level
if isinstance(R, ParameterObj):
reactants = R
else:
for r in R:
self.is_valid_entity_with_concentration(r)
self.has_non_zero_concentration(r)
entity, level = r
reactants.append((self.get_entity_id(entity), level))
if self.max_concentration < level:
self.max_concentration = level
#
# INHIBITORS
#
inhibitors = []
for i in I:
self.is_valid_entity_with_concentration(i)
self.has_non_zero_concentration(i)
entity, level = i
inhibitors.append((self.get_entity_id(entity), level))
if self.max_concentration < level:
self.max_concentration = level
if isinstance(I, ParameterObj):
inhibitors = I
else:
for i in I:
self.is_valid_entity_with_concentration(i)
self.has_non_zero_concentration(i)
entity, level = i
inhibitors.append((self.get_entity_id(entity), level))
if self.max_concentration < level:
self.max_concentration = level
#
# PRODUCTS
#
products = []
for p in P:
self.is_valid_entity_with_concentration(p)
self.has_non_zero_concentration(p)
entity, level = p
products.append((self.get_entity_id(entity), level))
if isinstance(P, ParameterObj):
products = P
else:
for p in P:
self.is_valid_entity_with_concentration(p)
self.has_non_zero_concentration(p)
entity, level = p
products.append((self.get_entity_id(entity), level))
return reactants, inhibitors, products
def is_parametric_reaction(self, reaction):
result = any([isinstance(r_set, ParameterObj) for r_set in reaction])
return result
def add_reaction(self, R, I, P):
"""Adds a reaction
@@ -119,7 +147,11 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
if P == []:
raise RuntimeError("No products defined")
reaction = self.process_rip(R,I,P)
self.reactions.append(reaction)
if self.is_parametric_reaction(reaction):
self.parametric_reactions.append(reaction)
else:
self.reactions.append(reaction)
def add_reaction_without_reactants(self, R, I, P):
"""Adds a reaction"""
@@ -174,10 +206,18 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
return s
def state_to_str(self, state):
s = ""
for ent,level in state:
s += self.get_entity_name(ent) + "=" + str(level) + ", "
s = s[:-2]
"""
If state is a parameter, we return
the string representation of the whole state
which should be the name of the parameter
"""
if isinstance(state, ParameterObj):
return str(state)
else:
s = ""
for ent,level in state:
s += self.get_entity_name(ent) + "=" + str(level) + ", "
s = s[:-2]
return s
def show_background_set(self):

4
rs_testing.py
View File

@@ -27,7 +27,7 @@ def trivial_param():
r.add_reaction([("x", 1)], [("c", 1)], [("y", 2)])
r.add_reaction([("y", 1)], [("c", 1)], [("z", 1)])
r.add_reaction([("z", 1)], [("c", 1)], [("final", 1)])
r.add_reaction(ParameterObj("P1"), [("c", 1)], [("final", 1)])
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("0")
@@ -43,7 +43,7 @@ def trivial_param():
BagDescription.f_TRUE(),
BagDescription.f_entity("final") >= 1)
smt_rsc.check_rsltl(formula=f2)
smt_rsc.check_rsltl(formula=f2, max_level=5)
def example44_param():

20
smt/smt_checker_rsc_param.py
View File

@@ -14,7 +14,7 @@ from logics import rsLTL_Encoder
# def simplify(x):
# return x
def MAX(a, b):
def z3_max(a, b):
return If(a > b, a, b)
class SmtCheckerRSCParam(object):
@@ -31,7 +31,6 @@ class SmtCheckerRSCParam(object):
self.initialise()
def initialise(self):
"""Initialises all the variables used by the checker"""
@@ -41,7 +40,6 @@ class SmtCheckerRSCParam(object):
# intermediate products:
self.v_improd = []
self.v_improd_for_entities = []
self.next_level_to_encode = 0
@@ -55,12 +53,10 @@ class SmtCheckerRSCParam(object):
self.verification_time = None
def reset(self):
"""Reinitialises the state of the checker"""
self.initialise()
self.initialise()
def prepare_all_variables(self):
"""Prepares all the variables"""
@@ -68,8 +64,7 @@ class SmtCheckerRSCParam(object):
self.prepare_state_variables()
self.prepare_context_variables()
self.prepare_intermediate_product_variables()
self.next_level_to_encode += 1
self.next_level_to_encode += 1
def prepare_context_variables(self):
"""Prepares all the context variables"""
@@ -82,7 +77,6 @@ class SmtCheckerRSCParam(object):
self.v_ctx.append(variables)
def prepare_state_variables(self):
"""Prepares all the state variables"""
@@ -95,7 +89,6 @@ class SmtCheckerRSCParam(object):
self.ca_state.append(Int("CA"+str(level)+"_state"))
def prepare_intermediate_product_variables(self):
"""
Prepares the intermediate product variables
@@ -261,16 +254,15 @@ class SmtCheckerRSCParam(object):
enc = None
if len(elements) == 1:
enc = MAX(0, elements[0])
enc = z3_max(0, elements[0])
elif len(elements) > 1:
enc = 0
for i in range(len(elements) - 1):
enc = MAX(enc, MAX(elements[i], elements[i + 1]))
enc = z3_max(enc, z3_max(elements[i], elements[i + 1]))
return enc
def enc_automaton_trans(self, level):
"""Encodes the transition relation for the context automaton"""
@@ -603,7 +595,7 @@ class SmtCheckerRSCParam(object):
print("Test: ", s)
self.solver.add(s)
result = self.solver.check()
if result == sat:
print("\n[+] " + colour_str(C_RED, "SAT at level=" + str(self.current_level)))