protocols::genetic_algorithm::GeneticAlgorithmBase Class Reference

#include <GeneticAlgorithm.hh>

Public Types
typedef EntityRandomizer::OP	EntityRandomizerOP
typedef Entity::OP	EntityOP
typedef Entity::COP	EntityCOP
typedef Entity::COPs	EntityCOPs
typedef Entity::CAP	EntityCAP
typedef Entity::CAPs	EntityCAPs
typedef utility::vector1 < EntityOP >::iterator	pop_iter
typedef utility::vector1 < EntityOP >::const_iterator	pop_const_iter
typedef utility::vector1 < EntityCOP >::const_iterator	pop_const_const_iter
typedef boost::unordered_map < EntityElements, EntityOP, Vec1Hash, EntityElementsEqual >	TraitEntityHashMap

Public Member Functions
	GeneticAlgorithmBase ()
virtual	~GeneticAlgorithmBase ()
virtual EntityOP	add_entity (EntityElements const &traits)
virtual EntityOP	add_entity (EntityOP entity)
virtual EntityOP	add_parent_entity (EntityElements const &traits)
virtual EntityOP	add_parent_entity (EntityOP entity)
virtual void	clear_parents ()
virtual void	add_parents_from_current_generation ()
virtual void	propagate_best_from_previous_generation (core::Size size=1, bool unique=true)
	add the best entities from the previous generation More...
virtual void	fill_with_random_entities (core::Size size=0)
virtual void	fill_with_perturbations_of_existing_entities (core::Size size=0)
virtual void	fill_by_crossover (core::Size size=0)
	add entities that are recombinants of fit parents More...
virtual void	fill_by_mutation (core::Size size=0)
	add entities that are mutants of fit parents More...
virtual void	evolve_next_generation ()
	progress to the next generation and generate new entities More...
virtual bool	current_generation_complete ()
virtual bool	complete ()
virtual core::Real	best_fitness_from_current_generation () const
virtual void	set_rand (EntityRandomizerOP r)
virtual void	set_max_generations (core::Size s)
virtual void	set_max_pop_size (core::Size s)
virtual void	set_num_to_propagate (core::Size s)
virtual void	set_frac_by_recomb (core::Real f)
virtual void	set_checkpoint_prefix (std::string const &p)
virtual void	set_checkpoint_write_interval (core::Size i)
virtual void	set_checkpoint_gzip (bool b)
virtual void	set_checkpoint_rename (bool b)
virtual EntityCAPs	best_entities (core::Size num)
	non-const to permit sort More...
virtual Entity const &	tournament_select (utility::vector1< EntityCOP > const &pvec) const
	pick two random entities from an unordered vector, return the one whose fitness is better More...
virtual TraitEntityHashMap &	entity_cache ()
virtual TraitEntityHashMap const &	entity_cache () const
virtual utility::vector1 < utility::vector1< EntityOP > > const &	generations () const
virtual EntityCOPs	population (core::Size gen_num) const
	true const (read-only) access to entity population: new vector of const pointers More...
virtual void	print_generation_statistics (std::ostream &os, core::Size gen_num) const
virtual void	print_population (std::ostream &) const
virtual void	print_cache (std::ostream &) const
virtual std::string	entities_checkpoint_filename (std::string suffix="") const
virtual bool	read_entities_checkpoint (bool overwrite=false)
	for checkpointing fitness cache More...
virtual bool	write_entities_checkpoint () const
	for checkpointing fitness cache More...
virtual std::string	generations_checkpoint_filename (std::string suffix="") const
virtual bool	write_generations_checkpoint () const
	This seems to duplicate the functionality of the Entity's write_checkpoint function... More...
virtual bool	read_generations_checkpoint ()
virtual bool	read_checkpoint ()
virtual void	rename_checkpoint_files () const
	allows the prevention of accidental reuse of checkpoint files More...
virtual EntityCOP	entity_template () const
virtual void	set_entity_template (EntityCOP entity)
virtual EntityOP	new_entity ()
core::Size	current_generation () const
core::Size	max_generations () const
core::Size	max_population_size () const
core::Size	number_to_propagate () const
core::Real	fraction_by_recombination () const
pop_iter	current_generation_begin ()
pop_iter	current_generation_end ()
pop_const_iter	current_generation_begin () const
pop_const_iter	current_generation_end () const
EntityOP	curr_gen_entity (core::Size index)
	retreive a particular entity for the current generation More...

Protected Member Functions
core::Size	checkpoint_write_interval () const

Private Attributes
utility::vector1 < utility::vector1< EntityOP > >	generations_
utility::vector1< EntityCOP >	parent_entities_
TraitEntityHashMap	entity_cache_
EntityRandomizerOP	entity_randomizer_
EntityCOP	entity_template_
core::Size	current_generation_
core::Size	max_generations_
core::Size	max_population_size_
core::Size	number_to_propagate_
core::Real	fraction_by_recombination_
std::string	checkpoint_prefix_
core::Size	checkpoint_write_interval_
bool	checkpoint_gzip_
bool	checkpoint_rename_

Member Typedef Documentation

typedef Entity::CAP protocols::genetic_algorithm::GeneticAlgorithmBase::EntityCAP

typedef Entity::CAPs protocols::genetic_algorithm::GeneticAlgorithmBase::EntityCAPs

typedef Entity::COP protocols::genetic_algorithm::GeneticAlgorithmBase::EntityCOP

typedef Entity::COPs protocols::genetic_algorithm::GeneticAlgorithmBase::EntityCOPs

typedef Entity::OP protocols::genetic_algorithm::GeneticAlgorithmBase::EntityOP

typedef EntityRandomizer::OP protocols::genetic_algorithm::GeneticAlgorithmBase::EntityRandomizerOP

typedef utility::vector1< EntityCOP >::const_iterator protocols::genetic_algorithm::GeneticAlgorithmBase::pop_const_const_iter

typedef utility::vector1< EntityOP >::const_iterator protocols::genetic_algorithm::GeneticAlgorithmBase::pop_const_iter

typedef utility::vector1< EntityOP >::iterator protocols::genetic_algorithm::GeneticAlgorithmBase::pop_iter

typedef boost::unordered_map< EntityElements , EntityOP, Vec1Hash, EntityElementsEqual > protocols::genetic_algorithm::GeneticAlgorithmBase::TraitEntityHashMap

Constructor & Destructor Documentation

protocols::genetic_algorithm::GeneticAlgorithmBase::GeneticAlgorithmBase

(

)

protocols::genetic_algorithm::GeneticAlgorithmBase::~GeneticAlgorithmBase ( )

virtual

References checkpoint_rename_, and rename_checkpoint_files().

Member Function Documentation

Entity::OP protocols::genetic_algorithm::GeneticAlgorithmBase::add_entity ( EntityElements const &  traits )

virtual

References current_generation_, entity_cache_, generations_, and new_entity().

Referenced by fill_by_crossover(), fill_by_mutation(), fill_with_perturbations_of_existing_entities(), fill_with_random_entities(), propagate_best_from_previous_generation(), and read_generations_checkpoint().

Entity::OP protocols::genetic_algorithm::GeneticAlgorithmBase::add_entity ( EntityOP  entity )

virtual

References current_generation_, entity_cache_, generations_, and runtime_assert.

Entity::OP protocols::genetic_algorithm::GeneticAlgorithmBase::add_parent_entity ( EntityElements const &  traits )

virtual

References entity_cache_, new_entity(), and parent_entities_.

Entity::OP protocols::genetic_algorithm::GeneticAlgorithmBase::add_parent_entity ( EntityOP  entity )

virtual

References entity_cache_, parent_entities_, and runtime_assert.

void protocols::genetic_algorithm::GeneticAlgorithmBase::add_parents_from_current_generation ( )

virtual

References current_generation_, generations_, parent_entities_, runtime_assert, and size().

Referenced by evolve_next_generation().

Entity::CAPs protocols::genetic_algorithm::GeneticAlgorithmBase::best_entities ( core::Size  num )

virtual

non-const to permit sort

returns variable number of best (const) entities via vector of pointers to them

References begin, current_generation_, end, and generations_.

core::Real protocols::genetic_algorithm::GeneticAlgorithmBase::best_fitness_from_current_generation ( ) const

virtual

References current_generation_, and generations_.

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::checkpoint_write_interval ( ) const

protected

References checkpoint_write_interval_.

Referenced by protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses().

void protocols::genetic_algorithm::GeneticAlgorithmBase::clear_parents ( )

virtual

References parent_entities_.

bool protocols::genetic_algorithm::GeneticAlgorithmBase::complete ( )

virtual

References current_generation_, current_generation_complete(), and max_generations_.

GeneticAlgorithmBase::EntityOP protocols::genetic_algorithm::GeneticAlgorithmBase::curr_gen_entity

(

core::Size

index

)

retreive a particular entity for the current generation

References current_generation_, and generations_.

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation ( ) const

inline

References current_generation_.

GeneticAlgorithmBase::pop_iter protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_begin

(

)

References current_generation_, and generations_.

Referenced by protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses().

GeneticAlgorithmBase::pop_const_iter protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_begin

(

)

const

References current_generation_, and generations_.

bool protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_complete ( )

virtual

References current_generation_, and generations_.

Referenced by complete().

GeneticAlgorithmBase::pop_iter protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_end

(

)

References current_generation_, and generations_.

Referenced by protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses().

GeneticAlgorithmBase::pop_const_iter protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_end

(

)

const

References current_generation_, and generations_.

std::string protocols::genetic_algorithm::GeneticAlgorithmBase::entities_checkpoint_filename ( std::string  suffix = "" ) const

virtual

References checkpoint_gzip_, checkpoint_prefix_, and filename().

Referenced by read_entities_checkpoint(), rename_checkpoint_files(), and write_entities_checkpoint().

GeneticAlgorithmBase::TraitEntityHashMap & protocols::genetic_algorithm::GeneticAlgorithmBase::entity_cache ( )

virtual

References entity_cache_.

GeneticAlgorithmBase::TraitEntityHashMap const & protocols::genetic_algorithm::GeneticAlgorithmBase::entity_cache ( ) const

virtual

References entity_cache_.

EntityCOP protocols::genetic_algorithm::GeneticAlgorithmBase::entity_template ( ) const

virtual

References entity_template_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::evolve_next_generation ( )

virtual

progress to the next generation and generate new entities

This method performs the following steps:

1. If parent entities were not already specified, sets the parents to the current generation
2. Increments the generation counter
3. Copies the best scoring entities from the previous generation to the new one
4. Generates new entities by crossover and/or mutation
5. Clears the parent entities now that they have been used

References add_parents_from_current_generation(), current_generation_, fill_by_crossover(), fill_by_mutation(), fraction_by_recombination_, generations_, max_population_size_, number_to_propagate_, parent_entities_, pop_size, and propagate_best_from_previous_generation().

void protocols::genetic_algorithm::GeneticAlgorithmBase::fill_by_crossover ( core::Size  size = 0 )

virtual

add entities that are recombinants of fit parents

References add_entity(), protocols::genetic_algorithm::Entity::clone(), current_generation_, entity_randomizer_, generations_, max_population_size_, parent_entities_, runtime_assert, and tournament_select().

Referenced by evolve_next_generation().

void protocols::genetic_algorithm::GeneticAlgorithmBase::fill_by_mutation ( core::Size  size = 0 )

virtual

add entities that are mutants of fit parents

References add_entity(), protocols::genetic_algorithm::Entity::clone(), current_generation_, entity_randomizer_, generations_, max_population_size_, parent_entities_, runtime_assert, and tournament_select().

Referenced by evolve_next_generation().

void protocols::genetic_algorithm::GeneticAlgorithmBase::fill_with_perturbations_of_existing_entities ( core::Size  size = 0 )

virtual

References add_entity(), current_generation_, entity_randomizer_, generations_, max_population_size_, protocols::genetic_algorithm::TR, and numeric::random::uniform().

void protocols::genetic_algorithm::GeneticAlgorithmBase::fill_with_random_entities ( core::Size  size = 0 )

virtual

References add_entity(), current_generation_, entity_randomizer_, generations_, and max_population_size_.

core::Real protocols::genetic_algorithm::GeneticAlgorithmBase::fraction_by_recombination ( ) const

inline

References fraction_by_recombination_.

utility::vector1< utility::vector1< EntityOP > > const & protocols::genetic_algorithm::GeneticAlgorithmBase::generations ( ) const

virtual

References generations_.

std::string protocols::genetic_algorithm::GeneticAlgorithmBase::generations_checkpoint_filename ( std::string  suffix = "" ) const

virtual

References checkpoint_gzip_, checkpoint_prefix_, and filename().

Referenced by read_generations_checkpoint(), rename_checkpoint_files(), and write_generations_checkpoint().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::max_generations ( ) const

inline

References max_generations_.

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::max_population_size ( ) const

inline

References max_population_size_.

Entity::OP protocols::genetic_algorithm::GeneticAlgorithmBase::new_entity ( )

virtual

References entity_template_.

Referenced by add_entity(), add_parent_entity(), and read_entities_checkpoint().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::number_to_propagate ( ) const

inline

References number_to_propagate_.

Entity::COPs protocols::genetic_algorithm::GeneticAlgorithmBase::population ( core::Size  gen_num ) const

virtual

true const (read-only) access to entity population: new vector of const pointers

true const (read-only) access to entity population

References generations_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::print_cache ( std::ostream &  os ) const

virtual

References end, and entity_cache_.

Referenced by write_entities_checkpoint().

void protocols::genetic_algorithm::GeneticAlgorithmBase::print_generation_statistics ( std::ostream &  os, core::Size  gen_num  ) const

virtual

References begin, end, and generations_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::print_population ( std::ostream &  os ) const

virtual

References begin, current_generation_, end, and generations_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::propagate_best_from_previous_generation ( core::Size  size = 1, bool  unique = true  )

virtual

add the best entities from the previous generation

References add_entity(), current_generation_, generations_, and runtime_assert.

Referenced by evolve_next_generation().

bool protocols::genetic_algorithm::GeneticAlgorithmBase::read_checkpoint ( )

virtual

References read_entities_checkpoint(), and read_generations_checkpoint().

bool protocols::genetic_algorithm::GeneticAlgorithmBase::read_entities_checkpoint ( bool  overwrite = false )

virtual

for checkpointing fitness cache

References checkpoint_prefix_, utility::io::izstream::close(), entities_checkpoint_filename(), entity_cache_, file, filename(), new_entity(), utility::io::izstream::open(), basic::t_debug, basic::t_info, and protocols::genetic_algorithm::TR.

Referenced by read_checkpoint().

bool protocols::genetic_algorithm::GeneticAlgorithmBase::read_generations_checkpoint ( )

virtual

References add_entity(), checkpoint_prefix_, current_generation_, file, filename(), generations_, generations_checkpoint_filename(), protocols::genetic_algorithm::EntityElementFactory::get_instance(), max_generations_, and runtime_assert.

Referenced by read_checkpoint().

void protocols::genetic_algorithm::GeneticAlgorithmBase::rename_checkpoint_files ( ) const

virtual

allows the prevention of accidental reuse of checkpoint files

References checkpoint_prefix_, entities_checkpoint_filename(), utility::file::file_exists(), generations_checkpoint_filename(), and suffix.

Referenced by ~GeneticAlgorithmBase().

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_gzip ( bool  b )

inlinevirtual

References protocols::match::upstream::b, and checkpoint_gzip_.

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_prefix ( std::string const &  p )

inlinevirtual

References checkpoint_prefix_.

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_rename ( bool  b )

inlinevirtual

References protocols::match::upstream::b, and checkpoint_rename_.

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_write_interval ( core::Size  i )

inlinevirtual

References checkpoint_write_interval_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::set_entity_template ( EntityCOP  entity )

virtual

References entity_template_.

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_frac_by_recomb ( core::Real  f )

inlinevirtual

References fraction_by_recombination_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::set_max_generations ( core::Size  s )

virtual

References generations_, and max_generations_.

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_max_pop_size ( core::Size  s )

inlinevirtual

References max_population_size_.

virtual void protocols::genetic_algorithm::GeneticAlgorithmBase::set_num_to_propagate ( core::Size  s )

inlinevirtual

References number_to_propagate_.

void protocols::genetic_algorithm::GeneticAlgorithmBase::set_rand ( EntityRandomizerOP  r )

virtual

References entity_randomizer_.

Entity const & protocols::genetic_algorithm::GeneticAlgorithmBase::tournament_select ( utility::vector1< EntityCOP > const &  pvec ) const

virtual

pick two random entities from an unordered vector, return the one whose fitness is better

References protocols::genetic_algorithm::Entity::fitness(), numeric::random::uniform(), and uniform().

Referenced by fill_by_crossover(), and fill_by_mutation().

bool protocols::genetic_algorithm::GeneticAlgorithmBase::write_entities_checkpoint ( ) const

virtual

for checkpointing fitness cache

References checkpoint_prefix_, entities_checkpoint_filename(), file, filename(), and print_cache().

Referenced by protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses().

bool protocols::genetic_algorithm::GeneticAlgorithmBase::write_generations_checkpoint ( ) const

virtual

This seems to duplicate the functionality of the Entity's write_checkpoint function...

References checkpoint_prefix_, file, filename(), generations_, generations_checkpoint_filename(), and j.

Referenced by protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses().

Member Data Documentation

bool protocols::genetic_algorithm::GeneticAlgorithmBase::checkpoint_gzip_

private

Referenced by entities_checkpoint_filename(), generations_checkpoint_filename(), and set_checkpoint_gzip().

std::string protocols::genetic_algorithm::GeneticAlgorithmBase::checkpoint_prefix_

private

Referenced by entities_checkpoint_filename(), generations_checkpoint_filename(), read_entities_checkpoint(), read_generations_checkpoint(), rename_checkpoint_files(), set_checkpoint_prefix(), write_entities_checkpoint(), and write_generations_checkpoint().

bool protocols::genetic_algorithm::GeneticAlgorithmBase::checkpoint_rename_

private

Referenced by set_checkpoint_rename(), and ~GeneticAlgorithmBase().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::checkpoint_write_interval_

private

Referenced by checkpoint_write_interval(), and set_checkpoint_write_interval().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::current_generation_

private

Referenced by add_entity(), add_parents_from_current_generation(), best_entities(), best_fitness_from_current_generation(), complete(), curr_gen_entity(), current_generation(), current_generation_begin(), current_generation_complete(), current_generation_end(), evolve_next_generation(), fill_by_crossover(), fill_by_mutation(), fill_with_perturbations_of_existing_entities(), fill_with_random_entities(), print_population(), propagate_best_from_previous_generation(), and read_generations_checkpoint().

TraitEntityHashMap protocols::genetic_algorithm::GeneticAlgorithmBase::entity_cache_

private

Referenced by add_entity(), add_parent_entity(), entity_cache(), print_cache(), and read_entities_checkpoint().

EntityRandomizerOP protocols::genetic_algorithm::GeneticAlgorithmBase::entity_randomizer_

private

Referenced by fill_by_crossover(), fill_by_mutation(), fill_with_perturbations_of_existing_entities(), fill_with_random_entities(), and set_rand().

EntityCOP protocols::genetic_algorithm::GeneticAlgorithmBase::entity_template_

private

Referenced by entity_template(), new_entity(), and set_entity_template().

core::Real protocols::genetic_algorithm::GeneticAlgorithmBase::fraction_by_recombination_

private

Referenced by evolve_next_generation(), fraction_by_recombination(), and set_frac_by_recomb().

utility::vector1< utility::vector1< EntityOP > > protocols::genetic_algorithm::GeneticAlgorithmBase::generations_

private

Referenced by add_entity(), add_parents_from_current_generation(), best_entities(), best_fitness_from_current_generation(), curr_gen_entity(), current_generation_begin(), current_generation_complete(), current_generation_end(), evolve_next_generation(), fill_by_crossover(), fill_by_mutation(), fill_with_perturbations_of_existing_entities(), fill_with_random_entities(), generations(), population(), print_generation_statistics(), print_population(), propagate_best_from_previous_generation(), read_generations_checkpoint(), set_max_generations(), and write_generations_checkpoint().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::max_generations_

private

Referenced by complete(), max_generations(), read_generations_checkpoint(), and set_max_generations().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::max_population_size_

private

Referenced by evolve_next_generation(), fill_by_crossover(), fill_by_mutation(), fill_with_perturbations_of_existing_entities(), fill_with_random_entities(), max_population_size(), and set_max_pop_size().

core::Size protocols::genetic_algorithm::GeneticAlgorithmBase::number_to_propagate_

private

Referenced by evolve_next_generation(), number_to_propagate(), and set_num_to_propagate().

utility::vector1< EntityCOP > protocols::genetic_algorithm::GeneticAlgorithmBase::parent_entities_

private

Referenced by add_parent_entity(), add_parents_from_current_generation(), clear_parents(), evolve_next_generation(), fill_by_crossover(), and fill_by_mutation().

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

• symlinks/rosetta/src/protocols/genetic_algorithm/GeneticAlgorithm.hh
• symlinks/rosetta/src/protocols/genetic_algorithm/GeneticAlgorithm.cc