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Fixing the encoding of reactions

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Artur Meski
2017-09-17 17:00:21 +01:00
parent 9297a7caf7
commit a43277c159
1 changed files with 39 additions and 33 deletions
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72
smt/smt_checker_rsc_param.py
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@@ -13,8 +13,8 @@ from logics import rsLTL_Encoder
from rs.reaction_system_with_concentrations_param import ParameterObj, is_param from rs.reaction_system_with_concentrations_param import ParameterObj, is_param
def simplify(x): # def simplify(x):
return x # return x
def z3_max(a, b): def z3_max(a, b):
return If(a > b, a, b) return If(a > b, a, b)
@@ -263,6 +263,7 @@ class SmtCheckerRSCParam(object):
param_name = reactants.name param_name = reactants.name
for entity in self.rs.set_of_bgset_ids: for entity in self.rs.set_of_bgset_ids:
enc_reactants = And(enc_reactants, Or( enc_reactants = And(enc_reactants, Or(
self.v_param[param_name][entity] == 0,
self.v[level][entity] >= self.v_param[param_name][entity], self.v[level][entity] >= self.v_param[param_name][entity],
self.v_ctx[level][entity] >= self.v_param[param_name][entity])) self.v_ctx[level][entity] >= self.v_param[param_name][entity]))
else: else:
@@ -277,8 +278,10 @@ class SmtCheckerRSCParam(object):
param_name = inhibitors.name param_name = inhibitors.name
for entity in self.rs.set_of_bgset_ids: for entity in self.rs.set_of_bgset_ids:
enc_inhibitors = And(enc_inhibitors, Or( enc_inhibitors = And(enc_inhibitors, Or(
self.v[level][entity] < self.v_param[param_name][entity], self.v_param[param_name][entity] == 0,
self.v_ctx[level][entity] < self.v_param[param_name][entity])) And(
self.v[level][entity] < self.v_param[param_name][entity],
self.v_ctx[level][entity] < self.v_param[param_name][entity])))
else: else:
for entity, conc in inhibitors: for entity, conc in inhibitors:
enc_inhibitors = And(enc_inhibitors, And( enc_inhibitors = And(enc_inhibitors, And(
@@ -290,18 +293,35 @@ class SmtCheckerRSCParam(object):
if is_param(products): if is_param(products):
param_name = products.name param_name = products.name
for entity in self.rs.set_of_bgset_ids: for entity in self.rs.set_of_bgset_ids:
enc_products = And(enc_products, enc_products = simplify(And(enc_products, Or(
self.v_improd[level + 1][reaction_id][entity] == self.v_param[param_name][entity]) self.v_param[param_name][entity] == 0,
self.v_improd[level + 1][reaction_id][entity] == self.v_param[param_name][entity])))
else: else:
for entity, conc in products: for entity, conc in products:
enc_products = And(enc_products, enc_products = simplify(And(enc_products,
self.v_improd[level + 1][reaction_id][entity] == conc) self.v_improd[level + 1][reaction_id][entity] == conc))
enc_no_prod = True
if is_param(products):
for entity in self.rs.set_of_bgset_ids:
enc_products = And(enc_products,
self.v_improd[level + 1][reaction_id][entity] == 0)
else:
for entity, _ in products:
enc_no_prod = simplify(And(enc_no_prod,
self.v_improd[level + 1][reaction_id][entity] == 0))
# #
# (R and I) iff P # (R and I) iff P
# #
enc_reaction = simplify( enc_enabled = And(enc_reactants, enc_inhibitors) == enc_products
And(enc_reactants, enc_inhibitors) == enc_products)
#
# ~(R and I) iff P_zero
#
enc_not_enabled = Not(And(enc_reactants, enc_inhibitors)) == enc_no_prod
enc_reaction = And(enc_enabled, enc_not_enabled)
return enc_reaction return enc_reaction
@@ -364,7 +384,8 @@ class SmtCheckerRSCParam(object):
# {products}[level+1] # {products}[level+1]
# #
current_v_improd_for_entities = self.v_improd_for_entities[level + 1] current_v_improd_for_entities = self.v_improd_for_entities[level + 1]
for entity, per_reaction_vars in current_v_improd_for_entities.items(): for entity in self.rs.set_of_bgset_ids:
per_reaction_vars = current_v_improd_for_entities.get(entity, [])
enc_max_prod = simplify( enc_max_prod = simplify(
And(enc_max_prod, self.v[level + 1][entity] == self.enc_max(per_reaction_vars))) And(enc_max_prod, self.v[level + 1][entity] == self.enc_max(per_reaction_vars)))
@@ -373,15 +394,18 @@ class SmtCheckerRSCParam(object):
enc_trans_with_max = simplify(And(enc_general_cond, enc_max_prod, enc_trans)) enc_trans_with_max = simplify(And(enc_general_cond, enc_max_prod, enc_trans))
print(enc_trans_with_max) # print(enc_trans_with_max)
return enc_trans_with_max return enc_trans_with_max
def enc_max(self, elements): def enc_max(self, elements):
enc = None enc = None
if elements == []:
enc = 0
if len(elements) == 1: elif len(elements) == 1:
enc = z3_max(0, elements[0]) enc = z3_max(0, elements[0])
elif len(elements) > 1: elif len(elements) > 1:
@@ -425,22 +449,6 @@ class SmtCheckerRSCParam(object):
raise RuntimeError("Should not be used with RSC") raise RuntimeError("Should not be used with RSC")
# enc = True
# used_entities_ids = self.rs.get_state_ids(state)
#
# for ent,conc in state:
# e_id = self.rs.get_entity_id(ent)
# enc = And(enc, self.v[level][e_id] == conc)
#
# not_in_state = set(range(len(self.rs.background_set)))
# not_in_state = not_in_state.difference(set(used_entities_ids))
#
# for entity in not_in_state:
# enc = And(enc, self.v[level][entity] == 0)
#
# return simplify(enc)
def enc_min_state(self, level, state): def enc_min_state(self, level, state):
"""Encodes the state at the given level with the minimal required concentration levels""" """Encodes the state at the given level with the minimal required concentration levels"""
@@ -454,8 +462,7 @@ class SmtCheckerRSCParam(object):
# for entity in state_ids: # for entity in state_ids:
# enc = And(enc, self.v[level][entity]) # enc = And(enc, self.v[level][entity])
return simplify(enc) return simplify(enc)
def enc_state_with_blocking(self, level, prop): def enc_state_with_blocking(self, level, prop):
"""Encodes the state at the given level with blocking certain concentrations""" """Encodes the state at the given level with blocking certain concentrations"""
@@ -472,7 +479,6 @@ class SmtCheckerRSCParam(object):
enc = And(enc, self.v[level][e_id] < conc) enc = And(enc, self.v[level][e_id] < conc)
return simplify(enc) return simplify(enc)
def decode_witness(self, max_level, print_model=False): def decode_witness(self, max_level, print_model=False):
@@ -597,7 +603,7 @@ class SmtCheckerRSCParam(object):
"[" + colour_str(C_BOLD, "+") + "] " + "[" + colour_str(C_BOLD, "+") + "] " +
colour_str( colour_str(
C_GREEN, "SAT at level=" + str(self.current_level))) C_GREEN, "SAT at level=" + str(self.current_level)))
print(self.solver.model()) # print(self.solver.model())
if print_witness: if print_witness:
print("\n{:=^70}".format("[ WITNESS ]")) print("\n{:=^70}".format("[ WITNESS ]"))
self.decode_witness(self.current_level) self.decode_witness(self.current_level)