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Permanency encoding. Allows preserving concentration levels for a specified entity. Permanency can also be inhibited.

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Artur Meski
2016-03-02 18:09:07 +01:00
parent 6ab5304628
commit 02606e32bf
4 changed files with 53 additions and 15 deletions
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46
rctsys.py
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@@ -374,15 +374,14 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def __init__(self):
self.reactions = []
self.meta_reactions = dict()
self.background_set = []
self.context_entities = []
self.reactions_by_prod = None
self.max_concentration = 0
self.max_conc_per_ent = dict()
self.reactions = []
self.meta_reactions = dict()
self.permanent_entities = dict()
self.background_set = []
self.context_entities = [] # legacy. to be removed
self.reactions_by_prod = None
self.max_concentration = 0
self.max_conc_per_ent = dict()
def add_bg_set_entity(self, e):
name = ""
@@ -430,7 +429,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
if elem[1] < 1:
raise RuntimeError("Unexpected concentration level in state: " + str(elem))
def check_rip(self, R, I, P, ignore_empty_R=False):
def process_rip(self, R, I, P, ignore_empty_R=False):
"""Chcecks concentration levels and converts entities names into their ids"""
if R == [] and not ignore_empty_R:
@@ -466,7 +465,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
if P == []:
raise RuntimeError("No products defined")
reaction = self.check_rip(R,I,P)
reaction = self.process_rip(R,I,P)
self.reactions.append(reaction)
def add_reaction_without_reactants(self, R, I, P):
@@ -474,13 +473,13 @@ class ReactionSystemWithConcentrations(ReactionSystem):
if P == []:
raise RuntimeError("No products defined")
reaction = self.check_rip(R,I,P,ignore_empty_R=True)
reaction = self.process_rip(R,I,P,ignore_empty_R=True)
self.reactions.append(reaction)
def add_reaction_inc(self, incr_entity, incrementer, R, I):
"""Adds a macro/meta reaction for increasing the value of incr_entity"""
reactants,inhibitors,products = self.check_rip(R,I,[],ignore_empty_R=True)
reactants,inhibitors,products = self.process_rip(R,I,[],ignore_empty_R=True)
incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id,[])
self.meta_reactions[incr_entity_id].append(("inc", self.get_entity_id(incrementer), reactants, inhibitors))
@@ -488,11 +487,22 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def add_reaction_dec(self, decr_entity, decrementer, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants,inhibitors,products = self.check_rip(R,I,[],ignore_empty_R=True)
reactants,inhibitors,products = self.process_rip(R,I,[],ignore_empty_R=True)
decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id,[])
self.meta_reactions[decr_entity_id].append(("dec", self.get_entity_id(decrementer), reactants, inhibitors))
def add_permanency(self, ent, I):
"""Sets entity to be permanent unless it is inhibited"""
ent_id = self.get_entity_id(ent)
if ent_id in self.permanent_entities:
raise RuntimeError("Permanency for {0} already defined.".format(ent))
inhibitors = self.process_rip([],I,[],ignore_empty_R=True)[1]
self.permanent_entities[ent_id] = inhibitors
def set_context_entities(self, entities):
raise NotImplementedError
@@ -535,9 +545,15 @@ class ReactionSystemWithConcentrations(ReactionSystem):
for e,max_conc in self.max_conc_per_ent.items():
print("\t - {0:>20} = {1:<6}".format(self.get_entity_name(e),max_conc))
def show_permanent_entities(self):
print("[*] Permanent entities:")
for e,inhibitors in self.permanent_entities.items():
print("\t - {0:>20}: {1:<6}".format(self.get_entity_name(e),"I={" + self.state_to_str(inhibitors) + "}"))
def show(self, soft=False):
self.show_background_set()
self.show_reactions(soft)
self.show_permanent_entities()
self.show_meta_reactions()
self.show_max_concentrations()