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cleanup

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Artur Meski
2017-09-03 15:13:23 +01:00
parent ac150b2744
commit a2dc2ec31f
1 changed files with 28 additions and 24 deletions
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40
rs/reaction_system_with_concentrations_param.py
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@@ -4,32 +4,35 @@ from colour import *
from rs.reaction_system import ReactionSystem from rs.reaction_system import ReactionSystem
class ParameterSet(object): class ParameterSet(object):
def __init__(self, name): def __init__(self, name):
self.name = name self.name = name
class ReactionSystemWithConcentrationsParam(ReactionSystem): class ReactionSystemWithConcentrationsParam(ReactionSystem):
def __init__(self): def __init__(self):
self.reactions = [] self.reactions = []
self.meta_reactions = dict() self.meta_reactions = dict()
self.permanent_entities = dict() self.permanent_entities = dict()
self.background_set = [] self.background_set = []
self.context_entities = [] # legacy. to be removed self.context_entities = [] # legacy. to be removed
self.reactions_by_prod = None self.reactions_by_prod = None
self.max_concentration = 0 self.max_concentration = 0
self.max_conc_per_ent = dict() self.max_conc_per_ent = dict()
def add_bg_set_entity(self, e): def add_bg_set_entity(self, e):
name = "" name = ""
def_max_conc = -1 def_max_conc = -1
if type(e) is tuple and len(e) == 2: if type(e) is tuple and len(e) == 2:
name,def_max_conc = e name, def_max_conc = e
elif type(e) is str: elif type(e) is str:
name = e name = e
print("\nWARNING: no maximal concentration level specified for:", e, "\n") print("\nWARNING: no maximal concentration level specified for:", e, "\n")
else: else:
raise RuntimeError("Bad entity type when adding background set element") raise RuntimeError(
"Bad entity type when adding background set element")
self.assume_not_in_bgset(name) self.assume_not_in_bgset(name)
self.background_set.append(name) self.background_set.append(name)
@@ -73,7 +76,8 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def has_non_zero_concentration(self, elem): def has_non_zero_concentration(self, elem):
if elem[1] < 1: if elem[1] < 1:
raise RuntimeError("Unexpected concentration level in state: " + str(elem)) raise RuntimeError(
"Unexpected concentration level in state: " + str(elem))
def process_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""" """Chcecks concentration levels and converts entities names into their ids"""
@@ -85,26 +89,26 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
for r in R: for r in R:
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
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
inhibitors = [] inhibitors = []
for i in I: for i in I:
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
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
products = [] products = []
for p in P: for p in P:
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
products.append((self.get_entity_id(entity),level)) products.append((self.get_entity_id(entity), level))
return reactants,inhibitors,products return reactants, inhibitors, products
def add_reaction(self, R, I, P): def add_reaction(self, R, I, P):
"""Adds a reaction """Adds a reaction