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protocols::genetic_algorithm::GeneticAlgorithm Class Reference

#include <GeneticAlgorithm.hh>

Inheritance diagram for protocols::genetic_algorithm::GeneticAlgorithm:
Inheritance graph
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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 TraitEntityHashMapentity_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
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::genetic_algorithm::GeneticAlgorithm::GeneticAlgorithm ( )
protocols::genetic_algorithm::GeneticAlgorithm::~GeneticAlgorithm ( )
overridedefault

Member Function Documentation

void protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses ( )
virtual
void protocols::genetic_algorithm::GeneticAlgorithm::set_func ( FitnessFunctionOP  f)
virtual

References fitness_function_.

Member Data Documentation

FitnessFunctionOP protocols::genetic_algorithm::GeneticAlgorithm::fitness_function_

Referenced by evaluate_fitnesses(), and set_func().


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