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Code re-formatting

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Artur Meski
2019-02-23 14:41:36 +00:00
parent 59cbc00e7f
commit c3a19d81dc
21 changed files with 1333 additions and 1016 deletions
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90
rs/reaction_system_with_concentrations_param.py
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@@ -3,20 +3,23 @@ from colour import *
from rs.reaction_system import ReactionSystem
class ParameterObj(object):
def __init__(self, name):
self.name = name
def __repr__(self):
return "@{0}".format(self.name)
def is_param(some_object):
if isinstance(some_object, ParameterObj):
return True
else:
return False
class ReactionSystemWithConcentrationsParam(ReactionSystem):
def __init__(self):
@@ -124,7 +127,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
reactants.append((self.get_entity_id(entity), level))
if self.max_concentration < level:
self.max_concentration = level
#
# INHIBITORS
#
@@ -139,7 +142,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
inhibitors.append((self.get_entity_id(entity), level))
if self.max_concentration < level:
self.max_concentration = level
#
# PRODUCTS
#
@@ -161,51 +164,56 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def add_reaction(self, R, I, P):
"""Adds a reaction
R, I, and P are sets of entities (not their IDs)
"""
if P == []:
raise RuntimeError("No products defined")
reaction = self.process_rip(R,I,P)
reaction = self.process_rip(R, I, P)
self.reactions.append(reaction)
def add_reaction_without_reactants(self, R, I, P):
"""Adds a reaction"""
if P == []:
raise RuntimeError("No products defined")
reaction = self.process_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.process_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))
self.meta_reactions.setdefault(incr_entity_id, [])
self.meta_reactions[incr_entity_id].append(
("inc", self.get_entity_id(incrementer), reactants, inhibitors))
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.process_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))
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]
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
@@ -233,33 +241,36 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
return str(state)
else:
s = ""
for ent,level in state:
for ent, level in state:
s += self.get_entity_name(ent) + "=" + str(level) + ", "
s = s[:-2]
return s
return s
def show_background_set(self):
print(C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
def show_meta_reactions(self):
print(C_MARK_INFO + " Meta reactions:")
for param_ent,reactions in self.meta_reactions.items():
for r_type,command,reactants,inhibitors in reactions:
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
if r_type == "inc" or r_type == "dec":
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + \
" ) Command=( " + self.get_entity_name(command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + " ) Command=( " + self.get_entity_name(
command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
def show_max_concentrations(self):
print(C_MARK_INFO + " Maximal allowed concentration levels:")
for e,max_conc in self.max_conc_per_ent.items():
print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e),max_conc))
for e, max_conc in self.max_conc_per_ent.items():
print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e), max_conc))
def show_permanent_entities(self):
print(C_MARK_INFO + " Permanent entities:")
for e,inhibitors in self.permanent_entities.items():
print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ","I={" + self.state_to_str(inhibitors) + "}"))
for e, inhibitors in self.permanent_entities.items():
print(" - {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()
@@ -268,21 +279,22 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.show_permanent_entities()
self.show_meta_reactions()
self.show_max_concentrations()
def get_producible_entities(self):
"""
Returns the set of entities that appear as products of
reactions.
"""
producible_entities = set()
for reaction in self.reactions:
product_entities = [e for e,c in reaction[2] if c > 0]
producible_entities = producible_entities.union(set(product_entities))
product_entities = [e for e, c in reaction[2] if c > 0]
producible_entities = producible_entities.union(
set(product_entities))
return producible_entities
def get_reaction_system(self):
"""
Translates RSC into RS