#include <GeneticAlgorithm.hh>

Inheritance diagram for protocols::genetic_algorithm::GeneticAlgorithm:

Public Types
typedef FitnessFunction::OP	FitnessFunctionOP

Public Types inherited from protocols::genetic_algorithm::GeneticAlgorithmBase
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
	GeneticAlgorithm ()

	~GeneticAlgorithm () override

virtual void	set_func (FitnessFunctionOP f)

virtual void	evaluate_fitnesses ()

Public Member Functions inherited from protocols::genetic_algorithm::GeneticAlgorithmBase
	GeneticAlgorithmBase ()

	~GeneticAlgorithmBase () override

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

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 ()

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...

Public Attributes
FitnessFunctionOP	fitness_function_

Additional Inherited Members
Protected Member Functions inherited from protocols::genetic_algorithm::GeneticAlgorithmBase
core::Size	checkpoint_write_interval () const