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Entity concentration validation (against its max)

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Artur Meski
2019-04-28 12:22:01 +01:00
parent 614817bf94
commit 390eda7e48
2 changed files with 26 additions and 4 deletions
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21
reactics-smt/rs/reaction_system_with_concentrations_param.py
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@@ -98,6 +98,24 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
return False return False
def is_valid_concentration_for_entity(self, entity, level):
"""Checks the concentration level for entity"""
e = self.get_entity_id(entity)
try:
max_conc = self.max_conc_per_ent[e]
except KeyError as _:
return True
if level > max_conc:
return False
return True
def terminate_on_invalid_concentration(self, entity, level):
if not self.is_valid_concentration_for_entity(entity, level):
print("FATAL. Invalid entity concentration: {:s}={:d}".format(entity, level))
exit(1)
def get_state_ids(self, state): def get_state_ids(self, state):
"""Returns entities of the given state without levels""" """Returns entities of the given state without levels"""
return [self.get_entity_id(e) for e in state] return [self.get_entity_id(e) for e in state]
@@ -124,6 +142,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.is_valid_entity_with_concentration(r) self.is_valid_entity_with_concentration(r)
self.has_non_zero_concentration(r) self.has_non_zero_concentration(r)
entity, level = r entity, level = r
self.terminate_on_invalid_concentration(entity, level)
reactants.append((self.get_entity_id(entity), level)) reactants.append((self.get_entity_id(entity), level))
if self.max_concentration < level: if self.max_concentration < level:
self.max_concentration = level self.max_concentration = level
@@ -139,6 +158,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.is_valid_entity_with_concentration(i) self.is_valid_entity_with_concentration(i)
self.has_non_zero_concentration(i) self.has_non_zero_concentration(i)
entity, level = i entity, level = i
self.terminate_on_invalid_concentration(entity, level)
inhibitors.append((self.get_entity_id(entity), level)) inhibitors.append((self.get_entity_id(entity), level))
if self.max_concentration < level: if self.max_concentration < level:
self.max_concentration = level self.max_concentration = level
@@ -154,6 +174,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.is_valid_entity_with_concentration(p) self.is_valid_entity_with_concentration(p)
self.has_non_zero_concentration(p) self.has_non_zero_concentration(p)
entity, level = p entity, level = p
self.terminate_on_invalid_concentration(entity, level)
products.append((self.get_entity_id(entity), level)) products.append((self.get_entity_id(entity), level))
return reactants, inhibitors, products return reactants, inhibitors, products

9
reactics-smt/rs_testing.py
View File

@@ -26,9 +26,9 @@ def run_tests(cmd_args):
# heat_shock_response_param(cmd_args) # heat_shock_response_param(cmd_args)
# simple_param(cmd_args) # simple_param(cmd_args)
param_gene_expression(cmd_args) # param_gene_expression(cmd_args)
# mutex_bench_main(cmd_args) mutex_bench_main(cmd_args)
def mutex_bench_main(cmd_args): def mutex_bench_main(cmd_args):
@@ -76,7 +76,8 @@ def mutex_param_bench(cmd_args):
r.add_bg_set_entity(E(ent,i)) r.add_bg_set_entity(E(ent,i))
for ent in shared_entities: for ent in shared_entities:
r.add_bg_set_entity((ent, 1)) max_conc = 2 if ent == "lock" else 1
r.add_bg_set_entity((ent, max_conc))
################################################### ###################################################
@@ -94,7 +95,7 @@ def mutex_param_bench(cmd_args):
r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)]) r.add_reaction([E("req",i)],[E("act",i)],[E("req",i)])
enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)] enter_inhib = [E("act",j) for j in range(n_proc) if i != j] + [("lock",1)]
r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",1)]) r.add_reaction([E("req",i),E("act",i)],enter_inhib,[E("in",i), ("lock",2)])
r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)]) r.add_reaction([E("in",i),E("act",i)],Inhib,[E("out",i), ("done",1)])
r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)]) r.add_reaction([E("in",i)],[E("act",i)],[E("in",i)])