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protocols::genetic_algorithm::Entity Class Reference

#include <Entity.hh>

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Public Types

typedef
utility::pointer::owning_ptr
< Entity > 		OP
 
typedef
utility::pointer::owning_ptr
< Entity const > 		COP
 
typedef
utility::pointer::access_ptr
< Entity const > 		CAP
 
typedef utility::vector1< COP > COPs
 
typedef utility::vector1< CAP > CAPs
 

Public Member Functions

 Entity ()
 
 Entity (Entity const &entity)
 
Entity const & operator= (Entity const &)
 
virtual ~Entity ()
 
 Entity (std::string const &line)
 
virtual OP clone () const
 
virtual void set_traits_size (core::Size size)
 
virtual void set_traits (EntityElements const &traits)
 
virtual EntityElements const & traits () const
 
virtual void set_entity_element (core::Size index, EntityElementOP element)
 
virtual void set_fitness (core::Real val)
 
virtual core::Real fitness () const
 
virtual bool fitness_valid () const
 
virtual bool operator== (Entity const &other) const
 
virtual bool operator< (Entity const &other) const
 
virtual void show (std::ostream &os) const
 
virtual void write_checkpoint (std::ostream &os) const
 
virtual bool read_checkpoint (std::istream &is)
 

Private Attributes

EntityElements traits_
 
core::Real fitness_
 
bool fitness_valid_
 

Detailed Description

Entity: a vector of EntityElements used to describe the state for a system under optimization.

Definition at line 116 of file Entity.hh.

Member Typedef Documentation

typedef utility::pointer::access_ptr< Entity const > protocols::genetic_algorithm::Entity::CAP

Definition at line 121 of file Entity.hh.

typedef utility::vector1< CAP > protocols::genetic_algorithm::Entity::CAPs

Definition at line 123 of file Entity.hh.

typedef utility::pointer::owning_ptr< Entity const > protocols::genetic_algorithm::Entity::COP

Definition at line 120 of file Entity.hh.

typedef utility::vector1< COP > protocols::genetic_algorithm::Entity::COPs

Definition at line 122 of file Entity.hh.

typedef utility::pointer::owning_ptr< Entity > protocols::genetic_algorithm::Entity::OP

Definition at line 119 of file Entity.hh.

Constructor & Destructor Documentation

protocols::genetic_algorithm::Entity::Entity ( )

Definition at line 155 of file Entity.cc.

Referenced by clone().

protocols::genetic_algorithm::Entity::Entity ( Entity const &  entity)

Definition at line 167 of file Entity.cc.

References traits_.

protocols::genetic_algorithm::Entity::~Entity ( )
virtual

Definition at line 209 of file Entity.cc.

protocols::genetic_algorithm::Entity::Entity ( std::string const &  line)

Definition at line 161 of file Entity.cc.

References read_checkpoint().

Member Function Documentation

Entity::OP protocols::genetic_algorithm::Entity::clone ( ) const
virtual

Reimplemented in protocols::multistate_design::MultiStateEntity< T >.

Definition at line 211 of file Entity.cc.

References Entity().

Referenced by protocols::pack_daemon::PackDaemon::compute_energy_for_assignment(), protocols::genetic_algorithm::GeneticAlgorithm::fill_by_crossover(), and protocols::genetic_algorithm::GeneticAlgorithm::fill_by_mutation().

core::Real protocols::genetic_algorithm::Entity::fitness ( ) const
virtual

Definition at line 264 of file Entity.cc.

References fitness_.

Referenced by operator<(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results(), protocols::dna::DnaInterfaceMultiStateDesign::output_results(), protocols::multistate_design::MultiStateEntity< T >::show(), show(), protocols::genetic_algorithm::GeneticAlgorithm::tournament_select(), and protocols::pack_daemon::MultistateFitnessFunction::update_entity_history().

bool protocols::genetic_algorithm::Entity::fitness_valid ( ) const
virtual

Definition at line 268 of file Entity.cc.

References fitness_valid_.

bool protocols::genetic_algorithm::Entity::operator< ( Entity const &  other) const
virtual

Definition at line 290 of file Entity.cc.

References fitness(), and fitness_.

Entity const & protocols::genetic_algorithm::Entity::operator= ( Entity const &  rhs)

Definition at line 184 of file Entity.cc.

References traits_.

bool protocols::genetic_algorithm::Entity::operator== ( Entity const &  other) const
virtual

Definition at line 272 of file Entity.cc.

References traits_.

bool protocols::genetic_algorithm::Entity::read_checkpoint ( std::istream &  is)
virtual

Reimplemented in protocols::multistate_design::MultiStateEntity< T >.

Definition at line 321 of file Entity.cc.

References fitness_, fitness_valid_, protocols::genetic_algorithm::EntityElementFactory::get_instance(), and traits_.

Referenced by Entity(), and protocols::multistate_design::MultiStateEntity< T >::read_checkpoint().

void protocols::genetic_algorithm::Entity::set_entity_element ( core::Size  index,
EntityElementOP  element 
)
virtual

Definition at line 245 of file Entity.cc.

References fitness_valid_, and traits_.

void protocols::genetic_algorithm::Entity::set_fitness ( core::Real  val)
virtual

Definition at line 259 of file Entity.cc.

References fitness_, and fitness_valid_.

Referenced by protocols::multistate_design::MultiStateFitnessFunction::evaluate(), and protocols::pack_daemon::MultistateFitnessFunction::evaluate().

void protocols::genetic_algorithm::Entity::set_traits ( EntityElements const &  traits)
virtual

Definition at line 226 of file Entity.cc.

References fitness_valid_, and traits_.

Referenced by protocols::genetic_algorithm::EntityRandomizer::crossover(), protocols::genetic_algorithm::DiscreteRandomizer::mutate(), and protocols::genetic_algorithm::PositionSpecificRandomizer::mutate().

void protocols::genetic_algorithm::Entity::set_traits_size ( core::Size  size)
virtual

Definition at line 213 of file Entity.cc.

References fitness_valid_, and traits_.

void protocols::genetic_algorithm::Entity::show ( std::ostream &  os) const
virtual

Reimplemented in protocols::multistate_design::MultiStateEntity< T >.

Definition at line 295 of file Entity.cc.

References core::sequence::end, fitness(), and traits().

Referenced by protocols::genetic_algorithm::operator<<().

EntityElements const & protocols::genetic_algorithm::Entity::traits ( ) const
virtual

Definition at line 255 of file Entity.cc.

References traits_.

Referenced by protocols::pack_daemon::EntityFunc::assign_entity_sequence_to_variables(), protocols::genetic_algorithm::EntityRandomizer::crossover(), protocols::multistate_design::MultiStatePacker::evaluate(), protocols::pack_daemon::PackDaemon::mark_entity_as_unimportant(), protocols::genetic_algorithm::DiscreteRandomizer::mutate(), protocols::genetic_algorithm::PositionSpecificRandomizer::mutate(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results(), protocols::dna::DnaInterfaceMultiStateDesign::output_results(), protocols::pack_daemon::PackDaemon::recreate_pose_for_entity(), protocols::pack_daemon::PackDaemon::select_rotamer_subset(), protocols::multistate_design::MultiStateEntity< T >::show(), and show().

void protocols::genetic_algorithm::Entity::write_checkpoint ( std::ostream &  os) const
virtual

Reimplemented in protocols::multistate_design::MultiStateEntity< T >.

Definition at line 308 of file Entity.cc.

References core::sequence::end, fitness_, and traits_.

Referenced by protocols::pack_daemon::MPIMultistateFitnessFunction::broadcast_entity_string(), and protocols::multistate_design::MultiStateEntity< T >::write_checkpoint().

Member Data Documentation

core::Real protocols::genetic_algorithm::Entity::fitness_
private

Definition at line 153 of file Entity.hh.

Referenced by fitness(), operator<(), read_checkpoint(), set_fitness(), and write_checkpoint().

bool protocols::genetic_algorithm::Entity::fitness_valid_
private

Definition at line 154 of file Entity.hh.

Referenced by fitness_valid(), read_checkpoint(), set_entity_element(), set_fitness(), set_traits(), and set_traits_size().

EntityElements protocols::genetic_algorithm::Entity::traits_
private

Definition at line 152 of file Entity.hh.

Referenced by Entity(), operator=(), operator==(), read_checkpoint(), set_entity_element(), set_traits(), set_traits_size(), traits(), and write_checkpoint().

The documentation for this class was generated from the following files:
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