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Resources reporting. Chain reaction benchmark, etc.

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Artur Meski
2016-02-24 22:49:40 +01:00
parent 9c7cbc74f7
commit 8a739b0760
5 changed files with 309 additions and 119 deletions
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82
rctsys.py
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@@ -452,7 +452,15 @@ class ReactionSystemWithConcentrations(ReactionSystem):
incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id,[])
self.meta_reactions[incr_entity_id].append(("inc", reactants, inhibitors))
def add_reaction_dec(self, incr_entity, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants,inhibitors,products = self.process_rip(R,I,[])
decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id,[])
self.meta_reactions[decr_entity_id].append(("dec", reactants, inhibitors))
def set_context_entities(self, entities):
raise NotImplementedError
@@ -482,10 +490,10 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def show_meta_reactions(self):
print("[*] Meta reactions:")
for incr_ent,reactions in self.meta_reactions.items():
for param_ent,reactions in self.meta_reactions.items():
for r_type,reactants,inhibitors in reactions:
if r_type == "inc":
print("\t - [ Type=" + repr(r_type) + " Parameter=( " + self.get_entity_name(incr_ent) + \
if r_type == "inc" or r_type == "dec":
print("\t - [ Type=" + repr(r_type) + " Parameter=( " + self.get_entity_name(param_ent) + \
" ) ] -- ( R={" + self.state_to_str(reactants) + "}, \tI={" + self.state_to_str(inhibitors) + "} )")
else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
@@ -552,39 +560,53 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.add_reaction(new_reactants,new_inhibitors,new_products)
for incr_ent,reactions in self.meta_reactions.items():
for param_ent,reactions in self.meta_reactions.items():
for r_type,reactants,inhibitors in reactions:
param_ent_name = self.get_entity_name(param_ent)
new_reactants = []
new_inhibitors = []
for ent,conc in reactants:
n = self.get_entity_name(ent) + "_" + str(conc)
rs.ensure_bg_set_entity(n)
new_reactants.append(n)
for ent,conc in inhibitors:
n = self.get_entity_name(ent) + "_" + str(conc)
rs.ensure_bg_set_entity(n)
new_inhibitors.append(n)
if r_type == "inc":
incr_ent_name = self.get_entity_name(incr_ent)
new_reactants = []
new_inhibitors = []
for ent,conc in reactants:
n = self.get_entity_name(ent) + "_" + str(conc)
rs.ensure_bg_set_entity(n)
new_reactants.append(n)
for ent,conc in inhibitors:
n = self.get_entity_name(ent) + "_" + str(conc)
rs.ensure_bg_set_entity(n)
new_inhibitors.append(n)
pre_conc = incr_ent_name + "_" + str(1)
rs.ensure_bg_set_entity(pre_conc)
# pre_conc -- predecessor concentration
# succ_conc -- successor concentration concentration
for i in range(1,self.max_concentration):
succ_conc = incr_ent_name + "_" + str(i+1)
rs.ensure_bg_set_entity(succ_conc)
pre_conc = param_ent_name + "_" + str(i)
rs.ensure_bg_set_entity(pre_conc)
new_products = []
for j in range(1,i+1):
new_p = incr_ent_name + "_" + str(j)
succ_value = i+1
for j in range(1,succ_value+1):
new_p = param_ent_name + "_" + str(j)
rs.ensure_bg_set_entity(new_p)
new_products.append(new_p)
new_products.append(succ_conc)
rs.add_reaction(new_reactants + [pre_conc], new_inhibitors, new_products)
pre_conc = succ_conc
elif r_type == "dec":
for i in range(1,self.max_concentration):
pre_conc = param_ent_name + "_" + str(i+1)
rs.ensure_bg_set_entity(pre_conc)
new_products = []
succ_value = i
for j in range(1,succ_value+1):
new_p = param_ent_name + "_" + str(j)
rs.ensure_bg_set_entity(new_p)
new_products.append(new_p)
rs.add_reaction(new_reactants + [pre_conc], new_inhibitors, new_products)
else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))