def generate_reactions(self, species_list):
'''
Generates the reactions by applying all reaction rules to given species
and generated species.
'''
result_list = []
rules = self.reaction_rules.copy()
sp_list = list(species_list)
for rule in rules.itervalues():
reactions = rule.generate_reactions(sp_list)
if len(reactions):
result = ReactionResult(rule)
for r in reactions:
result.add_reaction(r)
result_list.append(result)
return result_list
def generate_reaction_network(self, species_list, max_iteration=1):
'''
Generates the reaction network by applying all reaction rules
to the species given and generated in iterations.
species_list: The list of seed species.
max_iteration: The maximum number of the iteration.
'''
assert max_iteration > 0
# Reactions for each reaction ruls.
reaction_list_map = {}
for (rule_id, rule) in self.reaction_rules.iteritems():
reaction_list_map[rule_id] = []
# Initializes the list of species with given seed species.
sp_list = list(species_list)
# Loops until the list of species does not vary or up to the
# max iteration number.
for i in range(max_iteration):
# The counter for new species.
new_species_cnt = 0
# Finds the reaction rules and reactions.
results = self.generate_reactions(sp_list)
# Loops for the results.
for result in results:
rule = result.reaction_rule
# Loops for the reactions.
for reaction in result.reactions:
# Checks whether created reaction exists in the list
# of reactions.
exists = False
reaction_list = reaction_list_map[rule.id]
for r in reaction_list:
if r.equals(reaction):
exists = True
break
# If the created reaction is a new one, add it
# to the list of reactions.
if not exists:
reaction_list.append(reaction)
# Loops for the reactant species.
for p in reaction.products:
# Checks whether created species exists
# in the list of species.
exists = False
for sp in sp_list:
if p.equals(sp):
exists = True
break
# If the created species is a new one, add it
# to the species list.
if not exists:
sp_list.append(p)
new_species_cnt += 1
# If new species are not generated, breaks the loop.
if not new_species_cnt:
break
# Creates the returned value.
result_list = []
for (rule_id, reactions) in reaction_list_map.iteritems():
rule = self.reaction_rules[rule_id]
result = ReactionResult(rule)
for r in reactions:
result.add_reaction(r)
result_list.append(result)
return result_list
