Initial encoding of reactions
This commit is contained in:
Artur Meski
@@ -103,10 +103,15 @@ class SmtCheckerRSCParam(object):
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level = self.next_level_to_encode
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level = self.next_level_to_encode
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if level < 1:
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if level < 1:
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self.v_improd.append([])
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#
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# If we are at level==0, we add a dummy "level"
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# to match the indices of of the successors
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# which are always at level+1.
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#
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self.v_improd.append(None)
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else:
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else:
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variables = []
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reactions_dict = dict()
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number_of_reactions = len(self.rs.reactions)
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number_of_reactions = len(self.rs.reactions)
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for reaction in self.rs.reactions:
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for reaction in self.rs.reactions:
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@@ -120,13 +125,15 @@ class SmtCheckerRSCParam(object):
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str(reaction_id) + "_e" + str(entity))
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str(reaction_id) + "_e" + str(entity))
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entities_dict[entity] = varname
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entities_dict[entity] = varname
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variables.append(entities_dict)
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reactions_dict[reaction_id] = entities_dict
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self.v_improd.append(variables)
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self.v_improd.append(reactions_dict)
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print(self.v_improd)
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def enc_concentration_levels_assertion(self, level):
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def enc_concentration_levels_assertion(self, level):
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"""Encodes assertions that (some) variables need to be >0
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"""
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Encodes assertions that (some) variables need to be >0
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We do not need to actually control all the variables,
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We do not need to actually control all the variables,
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only those that can possibly go below 0.
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only those that can possibly go below 0.
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@@ -157,144 +164,7 @@ class SmtCheckerRSCParam(object):
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return init_state_enc
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return init_state_enc
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def enc_produced_concentration(self, level, prod_entity):
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"""Encodes the produced concentrations for the given level and entity"""
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rcts_for_prod_entity = []
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if prod_entity in self.rs.get_reactions_by_product():
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rcts_for_prod_entity = self.rs.get_reactions_by_product()[prod_entity]
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meta_reactions = []
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if prod_entity in self.rs.meta_reactions:
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meta_reactions = self.rs.meta_reactions[prod_entity]
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permanency_inhibition = None
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if prod_entity in self.rs.permanent_entities:
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permanency_inhibition = self.rs.permanent_entities[prod_entity]
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if rcts_for_prod_entity == [] and meta_reactions == []:
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return simplify(self.v[level+1][prod_entity] == 0) # this should never happen
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enc_enabledness = False
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# ----------- ordinary reactions --------------------------------------------
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enc_rct_prod = False
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enc_ordinary_reactions_enabledness = False
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for reactants,inhibitors,products in rcts_for_prod_entity:
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enc_reactants = True
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for reactant,concentration in reactants:
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
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enc_inhibitors = True
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for inhibitor,concentration in inhibitors:
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enc_inhibitors = simplify(And(enc_inhibitors,
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And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
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enc_rct_enabled = And(enc_reactants, enc_inhibitors)
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enc_products = self.v[level+1][products[0][0]] == products[0][1]
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enc_rct_prod = simplify(If(enc_rct_enabled, enc_products, enc_rct_prod))
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enc_enabledness = simplify(Or(enc_enabledness, enc_rct_enabled))
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enc_ordinary_reactions_enabledness = simplify(Or(enc_ordinary_reactions_enabledness,enc_rct_enabled))
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# for reactants,inhibitors,products in rcts_for_prod_entity:
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# enc_reactants = True
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# enc_inhibitors = True
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# # enc_products -- below
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#
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# for reactant,concentration in reactants:
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# enc_reactants = simplify(And(enc_reactants,
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# Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
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# for inhibitor,concentration in inhibitors:
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# enc_inhibitors = simplify(And(enc_inhibitors,
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# And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
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#
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# enc_products = self.v[level+1][products[0][0]] == products[0][1]
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#
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# enc_enabledness = simplify(Or(enc_enabledness, And(enc_reactants, enc_inhibitors)))
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# enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_reactants, enc_inhibitors, enc_products)))
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# -------- meta reactions ---------------------------------------------------
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for r_type,command_entity,reactants,inhibitors in meta_reactions:
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# command entity is e.g. 'inc' for incrementation operation
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# (inc,W) gives us the value W by which the given entity's value should be incremented
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enc_reactants = True
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enc_inhibitors = True
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for reactant,concentration in reactants:
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
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# command entity needs to be present (with concentration level > 0) in order to perform the operation
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][command_entity] > 0, self.v_ctx[level][command_entity] > 0)))
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for inhibitor,concentration in inhibitors:
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enc_inhibitors = simplify(And(enc_inhibitors,
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And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
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if r_type == "inc":
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value_after_inc = If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) + \
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If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity])
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enc_products = self.v[level+1][prod_entity] == value_after_inc
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elif r_type == "dec":
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value_after_dec = simplify(If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) - \
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If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity]))
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enc_products = self.v[level+1][prod_entity] == If(value_after_dec < 0, 0, value_after_dec)
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else:
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raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
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enc_meta_reaction_enabledness = And(enc_reactants, enc_inhibitors, Not(enc_ordinary_reactions_enabledness))
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enc_enabledness = simplify(Or(enc_enabledness, enc_meta_reaction_enabledness))
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enc_rct_prod = simplify(Or(enc_rct_prod, And(enc_meta_reaction_enabledness, enc_products)))
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# -----------------------------------------------------------------------------
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if not permanency_inhibition == None:
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enc_reactants = Or(self.v[level][prod_entity] >= concentration, self.v_ctx[level][prod_entity] >= concentration)
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enc_inhibitors = True
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for inhibitor,concentration in permanency_inhibition:
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enc_inhibitors = simplify(And(enc_inhibitors,
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And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
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enc_products = simplify(self.v[level+1][prod_entity] == \
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If(self.v[level][prod_entity] > self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]))
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enc_permanency_enabledness = And(enc_reactants, enc_inhibitors, Not(enc_ordinary_reactions_enabledness))
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enc_enabledness = simplify(Or(enc_enabledness, enc_permanency_enabledness))
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enc_permanency = And(enc_permanency_enabledness, enc_products)
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enc_rct_prod = simplify(Or(enc_rct_prod, enc_permanency))
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# -----------------------------------------------------------------------------
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enc_when_to_produce_zero_conc = simplify(And(Not(enc_enabledness), self.v[level+1][prod_entity] == 0))
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enc_rct_prod = Or(enc_rct_prod, enc_when_to_produce_zero_conc)
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return enc_rct_prod
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# def enc_entity_production(self, level, prod_entity):
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# """Encodes the production of a given entity from a given level at level+1"""
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#
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# enc_enab_cond = self.enc_enabledness(level, prod_entity)
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#
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# enc_ent_prod = Or(And(enc_enab_cond, self.v[level+1][prod_entity]),
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# And(Not(enc_enab_cond), Not(self.v[level+1][prod_entity])))
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#
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# return simplify(enc_ent_prod)
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def enc_transition_relation(self, level):
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def enc_transition_relation(self, level):
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return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
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return simplify(And(self.enc_rs_trans(level), self.enc_automaton_trans(level)))
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@@ -302,19 +172,54 @@ class SmtCheckerRSCParam(object):
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def enc_rs_trans(self, level):
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def enc_rs_trans(self, level):
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"""Encodes the transition relation"""
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"""Encodes the transition relation"""
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unused_entities = set(range(len(self.rs.background_set)))
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#
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# IMPORTANT NOTE
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#
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# We need to make sure we do something about the UNUSED ENTITIES
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# that is, those that are never produced.
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#
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# They should have concentration levels set to 0.
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#
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enc_trans = True
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enc_trans = True
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reactions = self.rs.get_reactions_by_product()
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for reaction in self.rs.reactions:
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meta_reactions = self.rs.meta_reactions
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reactants, inhibitors, products = reaction
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reaction_id = self.rs.reactions.index(reaction)
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enc_reactants = True
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for entity, conc in reactants:
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enc_reactants = And(enc_reactants,
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Or(self.v[level][entity] >= conc, self.v_ctx[level][entity] >= conc))
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enc_inhibitors = True
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for entity, conc in inhibitors:
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enc_inhibitors = And(enc_inhibitors,
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And(self.v[level][entity] < conc, self.v_ctx[level][entity] < conc))
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enc_products = True
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#
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#
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#
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for entity, conc in products:
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enc_products = And(enc_products,
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self.v_improd[level+1][reaction_id][entity] == conc)
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#
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# (R and I) iff P
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#
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enc_reaction = simplify(And(enc_reactants, enc_inhibitors) == enc_products)
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enc_trans = simplify(And(enc_trans, enc_reaction))
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print(enc_trans)
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for prod_entity in chain(reactions, meta_reactions):
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#
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unused_entities.discard(prod_entity)
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# TODO:
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enc_trans = simplify(And(enc_trans, self.enc_produced_concentration(level, prod_entity)))
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#
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# Max of all the produced concentrations for each entity/product...
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for prod_entity in unused_entities:
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enc_trans = simplify(And(enc_trans, self.v[level+1][prod_entity] == 0))
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return enc_trans
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return enc_trans
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