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transition relation with max calculation

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Artur Meski
2017-08-20 19:57:23 +01:00
parent 2b7d5e77dd
commit ce6a1f6f19
2 changed files with 50 additions and 43 deletions
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90
smt/smt_checker_rsc_param.py
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@@ -47,6 +47,7 @@ class SmtCheckerRSCParam(object):
self.next_level_to_encode = 0
self.producible_entities = self.rs.get_producible_entities()
self.improducible_entities = set(self.rs.get_state_ids(self.rs.background_set)) - self.producible_entities
self.loop_position = Int("loop_position")
@@ -141,9 +142,9 @@ class SmtCheckerRSCParam(object):
self.v_improd.append(reactions_dict)
self.v_improd_for_entities.append(all_entities_dict)
print(self.v_improd)
# print(self.v_improd)
print(self.v_improd_for_entities)
# print(self.v_improd_for_entities)
def enc_concentration_levels_assertion(self, level):
"""
@@ -162,26 +163,26 @@ class SmtCheckerRSCParam(object):
enc_nz = simplify(And(enc_nz, v >= 0, v_ctx >= 0, v <= e_max, v_ctx <= e_max))
return enc_nz
def enc_init_state(self, level):
"""Encodes the initial state at the given level"""
rs_init_state_enc = True
for v in self.v[level]:
rs_init_state_enc = simplify(And(rs_init_state_enc, v == 0)) # the initial concentration levels are zeroed
# the initial concentration levels are zeroed
rs_init_state_enc = simplify(And(rs_init_state_enc, v == 0))
ca_init_state_enc = self.ca_state[level] == self.ca.get_init_state_id()
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
return init_state_enc
def enc_transition_relation(self, level):
return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
def enc_transition_relation(self, level):
return simplify(
And(self.enc_rs_trans(level),
self.enc_automaton_trans(level)))
def enc_rs_trans(self, level):
"""Encodes the transition relation"""
@@ -191,68 +192,76 @@ class SmtCheckerRSCParam(object):
#
# We need to make sure we do something about the UNUSED ENTITIES
# that is, those that are never produced.
#
#
# They should have concentration levels set to 0.
#
enc_trans = True
for reaction in self.rs.reactions:
reactants, inhibitors, products = reaction
reaction_id = self.rs.reactions.index(reaction)
enc_reactants = True
for entity, conc in reactants:
enc_reactants = And(enc_reactants,
Or(self.v[level][entity] >= conc, self.v_ctx[level][entity] >= conc))
enc_reactants = And(enc_reactants, Or(
self.v[level][entity] >= conc, self.v_ctx[level][entity] >= conc))
enc_inhibitors = True
for entity, conc in inhibitors:
enc_inhibitors = And(enc_inhibitors,
And(self.v[level][entity] < conc, self.v_ctx[level][entity] < conc))
enc_inhibitors = And(enc_inhibitors, And(
self.v[level][entity] < conc, self.v_ctx[level][entity] < conc))
enc_products = True
#
#
#
for entity, conc in products:
enc_products = And(enc_products,
self.v_improd[level+1][reaction_id][entity] == conc)
enc_products = And(enc_products, self.v_improd[
level + 1][reaction_id][entity] == conc)
#
# (R and I) iff P
#
enc_reaction = simplify(And(enc_reactants, enc_inhibitors) == enc_products)
enc_reaction = simplify(
And(enc_reactants, enc_inhibitors) == enc_products)
enc_trans = simplify(And(enc_trans, enc_reaction))
print(enc_trans)
# print(enc_trans)
#
# TODO:
#
# Max of all the produced concentrations for each entity/product...
enc_max_prod = True
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():
# enc_max_single_ent = True
#sorted_vars_by_conc = sorted(per_reaction_vars, key=lambda conc_var: conc_var[0])
#list_of_vars = [v for c,v in sorted_vars_by_conc]
# sorted_vars_by_conc = sorted(per_reaction_vars, key=lambda conc_var: conc_var[0])
# list_of_vars = [v for c,v in sorted_vars_by_conc]
print(per_reaction_vars, "--->", self.enc_max(per_reaction_vars))
# print(per_reaction_vars, "--->", self.enc_max(per_reaction_vars))
enc_max_prod = simplify(
And(enc_max_prod, self.v[level + 1][entity] == self.enc_max(per_reaction_vars)))
for entity in self.improducible_entities:
enc_max_prod = simplify(
And(enc_max_prod, self.v[level + 1][entity] == 0))
enc_trans_with_max = simplify(And(enc_max_prod, enc_trans))
return enc_trans_with_max
return enc_trans
def enc_max(self, elements):
enc = None
if len(elements) == 1:
return MAX(0, elements[0])
enc = MAX(0, elements[0])
elif len(elements) > 1:
@@ -260,11 +269,8 @@ class SmtCheckerRSCParam(object):
for i in range(len(elements) - 1):
enc = MAX(enc, MAX(elements[i], elements[i + 1]))
return enc
return enc
else:
return None
def enc_automaton_trans(self, level):
"""Encodes the transition relation for the context automaton"""