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protocols::genetic_algorithm::Entity Class Reference

#include <Entity.hh>

Inheritance diagram for protocols::genetic_algorithm::Entity:
Inheritance graph
[legend]

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

◆ CAP

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

◆ CAPs

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

◆ COP

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

◆ COPs

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

◆ OP

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

Constructor & Destructor Documentation

◆ Entity() [1/3]

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

◆ Entity() [2/3]

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

References traits_.

◆ ~Entity()

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

◆ Entity() [3/3]

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

◆ clone()

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().

◆ fitness()

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

References fitness_.

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

◆ fitness_valid()

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

References fitness_valid_.

◆ operator<()

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

References fitness(), and fitness_.

◆ operator=()

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

References traits_.

◆ operator==()

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

References traits_.

◆ read_checkpoint()

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().

◆ set_entity_element()

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().

◆ set_fitness()

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

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

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

◆ set_traits()

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

References fitness_valid_, traits(), and traits_.

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

◆ set_traits_size()

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

References fitness_valid_, and traits_.

◆ show()

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().

◆ to_string()

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

References show().

◆ traits()

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::DiscreteRandomizer::mutate(), protocols::genetic_algorithm::PositionSpecificRandomizer::mutate(), protocols::genetic_algorithm::Mutate1Randomizer::mutate(), protocols::dna::DnaInterfaceMultiStateDesign::output_results(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results(), protocols::pack_daemon::PackDaemon::recreate_pose_for_entity(), protocols::pack_daemon::PackDaemon::select_rotamer_subset(), set_traits(), show(), and protocols::multistate_design::MultiStateEntity::show().

◆ traits_string()

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

References traits_.

◆ write_checkpoint()

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

◆ fitness_

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

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

◆ fitness_valid_

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().

◆ traits_

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().

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