rs package
This commit is contained in:
Artur Meski
182
rs/reaction_system.py
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182
rs/reaction_system.py
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from sys import exit
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from colour import *
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class ReactionSystem(object):
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def __init__(self):
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self.reactions = []
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self.background_set = []
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#self.reactions_by_agents = [] # each element is 'reactions_by_prod'
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self.reactions_by_prod = None
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## legacy:
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self.init_contexts = []
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self.context_entities = []
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def assume_not_in_bgset(self, name):
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if self.is_in_background_set(name):
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raise RuntimeError("The entity " + name + " is already on the list")
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def add_bg_set_entity(self, name):
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self.assume_not_in_bgset(name)
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self.background_set.append(name)
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def ensure_bg_set_entity(self, name):
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if not self.is_in_background_set(name):
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self.background_set.append(name)
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def add_bg_set_entities(self, elements):
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for e in elements:
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self.add_bg_set_entity(e)
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def is_in_background_set(self, entity):
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"""Checks if the given name is valid wrt the background set="""
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if entity in self.background_set:
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return True
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else:
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return False
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def get_entity_id(self, name):
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try:
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return self.background_set.index(name)
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except ValueError:
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print("Undefined background set entity: " + repr(name))
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exit(1)
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def get_state_ids(self, state):
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ids = []
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for entity in state:
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ids.append(self.get_entity_id(entity))
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return ids
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def get_entity_name(self, entity_id):
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"""Returns the string corresponding to the entity"""
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return self.background_set[entity_id]
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def add_reaction(self, R, I, P):
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"""Adds a reaction"""
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if R == [] or P == []:
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raise RuntimeError("No reactants or products defined")
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reactants = []
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for entity in R:
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reactants.append(self.get_entity_id(entity))
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inhibitors = []
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for entity in I:
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inhibitors.append(self.get_entity_id(entity))
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products = []
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for entity in P:
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products.append(self.get_entity_id(entity))
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self.reactions.append((reactants, inhibitors, products))
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def add_initial_context_set(self, context_set):
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if context_set == []:
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print("Empty context set is not allowed")
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raise
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integers = []
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for entity in context_set:
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if not entity in self.background_set:
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print("The entity", entity, "is not in the background set")
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raise
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else:
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integers.append(self.get_entity_id(entity))
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self.init_contexts.append(integers)
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def set_context_entities(self, entities):
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for entity in entities:
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entity_id = self.get_entity_id(entity)
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self.context_entities.append(entity_id)
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def entities_names_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += entity + ", "
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s = s[:-2]
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return s
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def entities_ids_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += self.get_entity_name(entity) + ", "
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s = s[:-2]
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return s
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def state_to_str(self, state):
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return self.entities_ids_set_to_str(state)
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def show_reactions(self, soft=False):
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print(C_MARK_INFO + " Reactions:")
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if soft and len(self.reactions) > 50:
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print(" -> there are more than 50 reactions (" + str(len(self.reactions)) + ")")
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else:
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print(" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants"," inhibitors"," products"))
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for reaction in self.reactions:
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# print("\t( R={" + self.state_to_str(reaction[0]) + "}, I={" + self.state_to_str(reaction[1]) + "}, P={" + self.state_to_str(reaction[2]) + "} )")
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print(" " + "- {0: ^35}{1: ^25}{2: ^15}".format("{ " + self.state_to_str(reaction[0]) + " }",
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" { " + self.state_to_str(reaction[1]) + " }",
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" { " + self.state_to_str(reaction[2]) + " }"))
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def show_background_set(self):
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print(C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
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def show_initial_contexts(self):
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if len(self.init_contexts) > 0:
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print(C_MARK_INFO + " Initial context sets:")
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for ctx in self.init_contexts:
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print(" - {" + self.entities_ids_set_to_str(ctx) + "}")
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def show_context_entities(self):
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if len(self.context_entities) > 0:
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print(C_MARK_INFO + " Context entities: " + self.entities_ids_set_to_str(self.context_entities))
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def show(self, soft=False):
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self.show_background_set()
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self.show_initial_contexts()
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self.show_reactions(soft)
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self.show_context_entities()
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def get_reactions_by_product(self):
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"""Sorts reactions by their products and returns a dictionary of products"""
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if self.reactions_by_prod != None:
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return self.reactions_by_prod
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producible_entities = set()
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for reaction in self.reactions:
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producible_entities = producible_entities.union(set(reaction[2]))
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reactions_by_prod = {}
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for prod_entity in producible_entities:
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reactions_by_prod[prod_entity] = []
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for reaction in self.reactions:
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if prod_entity in reaction[2]:
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reactions_by_prod[prod_entity].append([reaction[0],reaction[1]])
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# save in cache
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self.reactions_by_prod = reactions_by_prod
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return reactions_by_prod
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def sanity_check(self):
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"""Performs a sanity check on the defined reaction system"""
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if self.reactions == []:
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print("No reactions defined")
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exit(1)
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if self.background_set == []:
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print("Empty background set")
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exit(1)
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