protocols::genetic_algorithm::Entity Class Reference

#include <Entity.hh>

Inheritance diagram for protocols::genetic_algorithm::Entity:

Public Types
typedef utility::pointer::shared_ptr < Entity >	OP
typedef utility::pointer::shared_ptr < Entity const >	COP
typedef utility::pointer::weak_ptr < Entity const >	CAP
typedef utility::vector1< COP >	COPs
typedef utility::vector1< CAP >	CAPs

Public Member Functions
	Entity ()
	Entity (Entity const &entity)
Entity &	operator= (Entity const &)
	~Entity () override
	Entity (std::string const &line)
	construct Entity from std::string (e.g. from file) More...
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 std::string	to_string () const
virtual std::string	traits_string () 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.

Member Typedef Documentation

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

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

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

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

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

Constructor & Destructor Documentation

protocols::genetic_algorithm::Entity::Entity

(

)

protocols::genetic_algorithm::Entity::Entity

(

Entity const &

entity

)

References traits_.

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

overridedefault

protocols::genetic_algorithm::Entity::Entity

(

std::string const &

line

)

construct Entity from std::string (e.g. from file)

Note

Do not call this from derived classes unless you understand its limitations

References read_checkpoint().

Member Function Documentation

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

virtual

Reimplemented in protocols::multistate_design::MultiStateEntity.

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

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

virtual

References fitness_.

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

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

virtual

References fitness_valid_.

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

virtual

References fitness(), and fitness_.

Entity & protocols::genetic_algorithm::Entity::operator=

(

Entity const &

rhs

)

References traits_.

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

virtual

References traits_.

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

virtual

Reimplemented in protocols::multistate_design::MultiStateEntity.

References fitness_, fitness_valid_, and traits_.

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

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

virtual

References fitness_valid_, and traits_.

Referenced by protocols::genetic_algorithm::Mutate1Randomizer::mutate().

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

virtual

References fitness_, fitness_valid_, and protocols::hybridization::val.

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

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

virtual

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

References fitness_valid_, and traits_.

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

virtual

Reimplemented in protocols::multistate_design::MultiStateEntity.

References core::chemical::element::F, fitness(), and traits().

Referenced by protocols::genetic_algorithm::operator<<(), and to_string().

std::string protocols::genetic_algorithm::Entity::to_string ( ) const

virtual

References show().

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

virtual

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::Mutate1Randomizer::mutate(), 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::show(), and show().

std::string protocols::genetic_algorithm::Entity::traits_string ( ) const

virtual

References traits_.

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

virtual

Reimplemented in protocols::multistate_design::MultiStateEntity.

References fitness_, and traits_.

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

Member Data Documentation

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

private

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

bool protocols::genetic_algorithm::Entity::fitness_valid_

private

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

EntityElements protocols::genetic_algorithm::Entity::traits_

private

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

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

• src/protocols/genetic_algorithm/Entity.hh
• src/protocols/genetic_algorithm/Entity.cc