reaction_rule_vector const& query_reaction_rule(
species_id_type const& r1, species_id_type const& r2) const
{
typename second_order_reaction_rule_vector_map::const_iterator
i(second_order_cache_.find(std::make_pair(r1, r2)));
if (i == second_order_cache_.end())
{
const ecell4::Species sp1(r1), sp2(r2);
ecell4::Model::reaction_rule_container_type
reaction_rules_at_ecell4(
model_->query_reaction_rules(sp1, sp2));
if (reaction_rules_at_ecell4.size() == 0)
{
reaction_rules_at_ecell4.push_back(
create_repulsive_reaction_rule(sp1, sp2));
}
std::pair<typename second_order_reaction_rule_vector_map::iterator, bool>
x(second_order_cache_.insert(
std::make_pair(std::make_pair(r1, r2), reaction_rule_vector())));
for (std::vector<ecell4::ReactionRule>::const_iterator
it(reaction_rules_at_ecell4.begin());
it != reaction_rules_at_ecell4.end(); it++)
{
x.first->second.push_back(convert_reaction_rule_type(*it));
}
return x.first->second;
}
return i->second;
}
EGFRDSimulatorWrapper(
boost::shared_ptr<NetworkModel> model,
boost::shared_ptr<EGFRDWorld> world,
Integer dissociation_retry_moves = 3)
: model_(model), world_(world)
{
// set the log level for epdp as L_WARNING.
::LoggerManager::register_logger_manager(
"ecell.EGFRDSimulator",
boost::shared_ptr< ::LoggerManager>(
new ::LoggerManager("dummy", ::Logger::L_WARNING)));
const std::vector<Species> species((*model_).list_species());
for (std::vector<Species>::const_iterator
i(species.begin()); i != species.end(); ++i)
{
if (!(*world_).has_species(*i))
{
(*world_).add_species(*i);
}
}
for (NetworkModel::species_container_type::const_iterator
i(species.begin()); i != species.end(); ++i)
{
for (NetworkModel::species_container_type::const_iterator
j(i); j != species.end(); ++j)
{
if ((*model_).query_reaction_rules(*i, *j).size() == 0)
{
(*world_).add_reaction_rule(
create_repulsive_reaction_rule(*i, *j));
}
}
}
const NetworkModel::reaction_rule_container_type&
reaction_rules((*model_).reaction_rules());
for (NetworkModel::reaction_rule_container_type::const_iterator
i(reaction_rules.begin()); i != reaction_rules.end(); ++i)
{
(*world_).add_reaction_rule(*i);
}
sim_ = boost::shared_ptr<simulator_type>(
(*world_).create_simulator(dissociation_retry_moves));
initialize();
}
