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cleanup

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Artur Meski
2017-09-03 15:15:26 +01:00
parent a2dc2ec31f
commit 2957a7ac52
1 changed files with 67 additions and 54 deletions
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71
rs/reaction_system_with_concentrations_param.py
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@@ -277,44 +277,44 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs = ReactionSystem() rs = ReactionSystem()
for reactants,inhibitors,products in self.reactions: for reactants, inhibitors, products in self.reactions:
new_reactants = [] new_reactants = []
new_inhibitors = [] new_inhibitors = []
new_products = [] new_products = []
for ent,conc in reactants: for ent, conc in reactants:
n = self.get_entity_name(ent) + "#" + str(conc) n = self.get_entity_name(ent) + "#" + str(conc)
rs.ensure_bg_set_entity(n) rs.ensure_bg_set_entity(n)
new_reactants.append(n) new_reactants.append(n)
for ent,conc in inhibitors: for ent, conc in inhibitors:
n = self.get_entity_name(ent) + "#" + str(conc) n = self.get_entity_name(ent) + "#" + str(conc)
rs.ensure_bg_set_entity(n) rs.ensure_bg_set_entity(n)
new_inhibitors.append(n) new_inhibitors.append(n)
for ent,conc in products: for ent, conc in products:
for i in range(1,conc+1): for i in range(1, conc + 1):
n = self.get_entity_name(ent) + "#" + str(i) n = self.get_entity_name(ent) + "#" + str(i)
rs.ensure_bg_set_entity(n) rs.ensure_bg_set_entity(n)
new_products.append(n) new_products.append(n)
rs.add_reaction(new_reactants,new_inhibitors,new_products) rs.add_reaction(new_reactants, new_inhibitors, new_products)
for param_ent,reactions in self.meta_reactions.items(): for param_ent, reactions in self.meta_reactions.items():
for r_type,command,reactants,inhibitors in reactions: for r_type, command, reactants, inhibitors in reactions:
param_ent_name = self.get_entity_name(param_ent) param_ent_name = self.get_entity_name(param_ent)
new_reactants = [] new_reactants = []
new_inhibitors = [] new_inhibitors = []
for ent,conc in reactants: for ent, conc in reactants:
n = self.get_entity_name(ent) + "#" + str(conc) n = self.get_entity_name(ent) + "#" + str(conc)
rs.ensure_bg_set_entity(n) rs.ensure_bg_set_entity(n)
new_reactants.append(n) new_reactants.append(n)
for ent,conc in inhibitors: for ent, conc in inhibitors:
n = self.get_entity_name(ent) + "#" + str(conc) n = self.get_entity_name(ent) + "#" + str(conc)
rs.ensure_bg_set_entity(n) rs.ensure_bg_set_entity(n)
new_inhibitors.append(n) new_inhibitors.append(n)
@@ -323,10 +323,12 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
if command in self.max_conc_per_ent: if command in self.max_conc_per_ent:
max_cmd_c = self.max_conc_per_ent[command] max_cmd_c = self.max_conc_per_ent[command]
else: else:
print("WARNING:\n\tThere is no maximal concentration level defined for " + self.get_entity_name(command)) print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(command))
print("\tThis is a very bad idea -- expect degraded performance\n") print("\tThis is a very bad idea -- expect degraded performance\n")
for l in range(1,max_cmd_c+1): for l in range(1, max_cmd_c + 1):
cmd_ent = self.get_entity_name(command) + "#" + str(l) cmd_ent = self.get_entity_name(command) + "#" + str(l)
rs.ensure_bg_set_entity(cmd_ent) rs.ensure_bg_set_entity(cmd_ent)
@@ -336,49 +338,60 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
# pre_conc -- predecessor concentration # pre_conc -- predecessor concentration
# succ_conc -- successor concentration concentration # succ_conc -- successor concentration concentration
for i in range(1,self.max_concentration): for i in range(1, self.max_concentration):
pre_conc = param_ent_name + "#" + str(i) pre_conc = param_ent_name + "#" + str(i)
rs.ensure_bg_set_entity(pre_conc) rs.ensure_bg_set_entity(pre_conc)
new_products = [] new_products = []
succ_value = i+l succ_value = i + l
for j in range(1,succ_value+1): for j in range(1, succ_value + 1):
if j > self.max_concentration: break if j > self.max_concentration:
break
new_p = param_ent_name + "#" + str(j) new_p = param_ent_name + "#" + str(j)
rs.ensure_bg_set_entity(new_p) rs.ensure_bg_set_entity(new_p)
new_products.append(new_p) new_products.append(new_p)
if new_products != []: if new_products != []:
rs.add_reaction(set(new_reactants + [pre_conc,cmd_ent]), set(new_inhibitors), set(new_products)) rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
elif r_type == "dec": elif r_type == "dec":
for i in range(1,self.max_concentration+1): for i in range(1, self.max_concentration + 1):
pre_conc = param_ent_name + "#" + str(i) pre_conc = param_ent_name + "#" + str(i)
rs.ensure_bg_set_entity(pre_conc) rs.ensure_bg_set_entity(pre_conc)
new_products = [] new_products = []
succ_value = i-l succ_value = i - l
for j in range(1,succ_value+1): for j in range(1, succ_value + 1):
if j > self.max_concentration: break if j > self.max_concentration:
break
new_p = param_ent_name + "#" + str(j) new_p = param_ent_name + "#" + str(j)
rs.ensure_bg_set_entity(new_p) rs.ensure_bg_set_entity(new_p)
new_products.append(new_p) new_products.append(new_p)
if new_products != []: if new_products != []:
rs.add_reaction(set(new_reactants + [pre_conc,cmd_ent]), set(new_inhibitors), set(new_products)) rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
else: else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type)) raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
for ent,inhibitors in self.permanent_entities.items(): for ent, inhibitors in self.permanent_entities.items():
max_c = self.max_concentration max_c = self.max_concentration
if ent in self.max_conc_per_ent: if ent in self.max_conc_per_ent:
max_c = self.max_conc_per_ent[ent] max_c = self.max_conc_per_ent[ent]
else: else:
print("WARNING:\n\tThere is no maximal concentration level defined for " + self.get_entity_name(ent)) print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(ent))
print("\tThis is a very bad idea -- expect degraded performance\n") print("\tThis is a very bad idea -- expect degraded performance\n")
def e_value(i): def e_value(i):
return self.get_entity_name(ent) + "#" + str(i) return self.get_entity_name(ent) + "#" + str(i)
for value in range(1,max_c+1): for value in range(1, max_c + 1):
new_reactants = [] new_reactants = []
new_inhibitors = [] new_inhibitors = []
@@ -386,15 +399,15 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
new_reactants = [e_value(value)] new_reactants = [e_value(value)]
for e_inh,conc in inhibitors: for e_inh, conc in inhibitors:
n = self.get_entity_name(e_inh) + "#" + str(conc) n = self.get_entity_name(e_inh) + "#" + str(conc)
rs.ensure_bg_set_entity(n) rs.ensure_bg_set_entity(n)
new_inhibitors.append(n) new_inhibitors.append(n)
for i in range(1,value+1): for i in range(1, value + 1):
new_products.append(e_value(i)) new_products.append(e_value(i))
rs.add_reaction(new_reactants,new_inhibitors,new_products) rs.add_reaction(new_reactants, new_inhibitors, new_products)
return rs return rs