@ Summarizes and contains all Individuals of one generation More...

#include <Population.hh>

Public Member Functions
	Population ()=default

	~Population ()=default

void	initialize_from_evotoptions (EvolutionOptions const &options, FragmentLibrary const &library, Scorer const &scorer)
	initializes setting from options object More...

utility::vector1< Individual > const &	individuals () const
	Exposes the individuals vector for const iterator access. More...

utility::vector1< Individual > &	individuals ()
	Expose the individuals vector for normal iterator access. More...

void	sort ()
	Sorts all individuals depending on their score. More...

bool	is_sorted ()
	Returns true if the individuals are sorted with lowest (and therefore best) score first. More...

core::Size	size () const
	Returns the size of this population. More...

void	set_supported_size (core::Size supported_size)
	Sets the supported size of this population. It will get reduced to this size through selective pressure. More...

Individual const &	individual (core::Size index) const
	Access specific individual. More...

Individual &	individual (core::Size index)
	Non-const access specific individual. More...

void	add_random (core::Size n_random_individuals, FragmentLibrary const &lib)
	Adds random individuals to a population. More...

void	add_individuals (utility::vector1< Individual > const &new_individuals)
	Adds new (and potentially unscored individuals to the population) More...

void	add_individuals (utility::vector1< LigandIdentifier > const &new_individuals)
	Adds new individuals based on provided LigandIdentifiers. More...

void	next_generation (Selector const &selector)
	Removes unselected individuals, raises the generation counter and sorts individuals. More...

void	add_individual (Individual const &individual)
	Adds an individual to this population and sets its id. More...

core::Size	generation () const
	Returns the current generation. More...

utility::vector1< Individual >	remove_individuals (utility::vector1< core::Size > indices)
	Removes individuals with the given index and returns them. More...

utility::vector1< Individual >	individuals (utility::vector1< core::Size > const &indices)
	Returns a copy of selected individuals. More...

void	replace_population (utility::vector1< Individual > const &individuals)
	Replaces the internal population with a new one. More...

utility::vector1< utility::vector1< core::Size > > const &	expose_generation_log () const
	For debugging and benchmarking purpose to observe population development. More...

utility::vector1< std::pair< core::Size, core::Size > > const &	expose_inheritance_graph () const
	For debugging and benchmarking purpose to observe population development. More...

Private Member Functions
bool	check_sorting ()
	Updates and returns the sorting state. Shouldn't be needed to be called usually. More...

void	log_generation ()
	Saves ids of all sorted individuals. More...

void	expand_inheritance_graph (Individual const &individual)
	Saves the data of the given individual in the inheritance graph. More...

Private Attributes
utility::vector1< Individual >	individuals_

core::Size	generation_ = 0

bool	sorting_guaranteed_ = false

core::Size	next_id_ = 1
	Keeps track of the next available and unused id. More...

core::Size	supported_size_ = 0

utility::vector1< utility::vector1< core::Size > >	generation_log_

utility::vector1< std::pair< core::Size, core::Size > >	inheritance_graph_
	For debugging and benchmarking purposes. Each entry represents a node in an inheritance graph First is child, second is the parent. If more than one parent is present, more than one entry is created. More...

Detailed Description

@ Summarizes and contains all Individuals of one generation

Constructor & Destructor Documentation

◆ Population()

protocols::ligand_evolution::Population::Population ( )

default

◆ ~Population()

protocols::ligand_evolution::Population::~Population ( )

default

Member Function Documentation

◆ add_individual()

void protocols::ligand_evolution::Population::add_individual ( Individual const & individual )

Adds an individual to this population and sets its id.

References expand_inheritance_graph(), individual(), individuals_, next_id_, and sorting_guaranteed_.

Referenced by add_individuals(), and add_random().

◆ add_individuals() [1/2]

void protocols::ligand_evolution::Population::add_individuals ( utility::vector1< Individual > const & new_individuals )

Adds new (and potentially unscored individuals to the population)

References add_individual(), individual(), size(), and protocols::TR().

Referenced by add_individuals(), initialize_from_evotoptions(), and replace_population().

◆ add_individuals() [2/2]

void protocols::ligand_evolution::Population::add_individuals ( utility::vector1< LigandIdentifier > const & new_individuals )

Adds new individuals based on provided LigandIdentifiers.

References add_individuals().

◆ add_random()

void protocols::ligand_evolution::Population::add_random	(	core::Size	n_random_individuals,
		FragmentLibrary const &	lib
	)

Adds random individuals to a population.

References add_individual(), individual(), and protocols::ligand_evolution::FragmentLibrary::random_ligand().

Referenced by initialize_from_evotoptions().

◆ check_sorting()

bool protocols::ligand_evolution::Population::check_sorting ( )

private

Updates and returns the sorting state. Shouldn't be needed to be called usually.

References individual(), individuals_, protocols::ligand_evolution::Individual::is_scored(), protocols::ligand_evolution::Individual::score(), and sorting_guaranteed_.

Referenced by is_sorted().

◆ expand_inheritance_graph()

void protocols::ligand_evolution::Population::expand_inheritance_graph ( Individual const & individual )

private

Saves the data of the given individual in the inheritance graph.

References protocols::ligand_evolution::Individual::id(), individual(), inheritance_graph_, and protocols::ligand_evolution::Individual::parents().

Referenced by add_individual().

◆ expose_generation_log()

utility::vector1< utility::vector1< core::Size > > const & protocols::ligand_evolution::Population::expose_generation_log ( ) const

For debugging and benchmarking purpose to observe population development.

References generation_log_.

Referenced by protocols::ligand_evolution::EvolutionManager::write_population_information().

◆ expose_inheritance_graph()

utility::vector1< std::pair< core::Size, core::Size > > const & protocols::ligand_evolution::Population::expose_inheritance_graph ( ) const

For debugging and benchmarking purpose to observe population development.

References inheritance_graph_.

Referenced by protocols::ligand_evolution::EvolutionManager::write_population_information().

◆ generation()

core::Size protocols::ligand_evolution::Population::generation ( ) const

Returns the current generation.

References generation_.

◆ individual() [1/2]

Individual & protocols::ligand_evolution::Population::individual ( core::Size index )

Non-const access specific individual.

References individuals_, and sorting_guaranteed_.

◆ individual() [2/2]

Individual const & protocols::ligand_evolution::Population::individual ( core::Size index ) const

Access specific individual.

References individuals_.

Referenced by add_individual(), add_individuals(), add_random(), protocols::ligand_evolution::RouletteSelector::apply(), protocols::ligand_evolution::EvolutionManager::calculate_quantiles(), check_sorting(), expand_inheritance_graph(), protocols::ligand_evolution::EvolutionManager::run(), and protocols::ligand_evolution::Scorer::score_population().

◆ individuals() [1/3]

utility::vector1< Individual > & protocols::ligand_evolution::Population::individuals ( )

Expose the individuals vector for normal iterator access.

References individuals_, and sorting_guaranteed_.

◆ individuals() [2/3]

utility::vector1< Individual > const & protocols::ligand_evolution::Population::individuals ( ) const

Exposes the individuals vector for const iterator access.

References individuals_.

Referenced by protocols::ligand_evolution::ElitistSelector::apply(), protocols::ligand_evolution::RouletteSelector::apply(), protocols::ligand_evolution::TournamentSelector::apply(), replace_population(), protocols::ligand_evolution::Scorer::score_population(), and protocols::ligand_evolution::EvolutionManager::scores_to_str().

◆ individuals() [3/3]

utility::vector1< Individual > protocols::ligand_evolution::Population::individuals ( utility::vector1< core::Size > const & indices )

Returns a copy of selected individuals.

References individuals_.

◆ initialize_from_evotoptions()

void protocols::ligand_evolution::Population::initialize_from_evotoptions	(	EvolutionOptions const &	options,
		FragmentLibrary const &	library,
		Scorer const &	scorer
	)

initializes setting from options object

References add_individuals(), add_random(), protocols::ligand_evolution::Scorer::get_best_loaded(), protocols::ligand_evolution::EvolutionOptions::get_pop_init_options(), protocols::ligand_evolution::EvolutionOptions::get_population_supported_size(), core::scoring::pair, set_supported_size(), and protocols::TR().

Referenced by protocols::ligand_evolution::EvolutionManager::init().

◆ is_sorted()

bool protocols::ligand_evolution::Population::is_sorted ( )

Returns true if the individuals are sorted with lowest (and therefore best) score first.

References check_sorting(), and sorting_guaranteed_.

Referenced by sort().

◆ log_generation()

void protocols::ligand_evolution::Population::log_generation ( )

private

Saves ids of all sorted individuals.

References generation_log_, individuals_, size(), and sort().

Referenced by next_generation().

◆ next_generation()

void protocols::ligand_evolution::Population::next_generation ( Selector const & selector )

Removes unselected individuals, raises the generation counter and sorts individuals.

References protocols::ligand_evolution::Selector::apply(), generation_, log_generation(), replace_population(), size(), sort(), supported_size_, and protocols::TR().

Referenced by protocols::ligand_evolution::EvolutionManager::run().

◆ remove_individuals()

utility::vector1< Individual > protocols::ligand_evolution::Population::remove_individuals ( utility::vector1< core::Size > indices )

Removes individuals with the given index and returns them.

References individuals_, protocols::mean_field::min(), size(), and protocols::TR().

Referenced by protocols::ligand_evolution::ElitistSelector::apply(), protocols::ligand_evolution::RouletteSelector::apply(), and protocols::ligand_evolution::TournamentSelector::apply().

◆ replace_population()

void protocols::ligand_evolution::Population::replace_population ( utility::vector1< Individual > const & individuals )

Replaces the internal population with a new one.

References add_individuals(), individuals(), and individuals_.

Referenced by next_generation(), and protocols::ligand_evolution::EvolutionManager::run().

◆ set_supported_size()

void protocols::ligand_evolution::Population::set_supported_size ( core::Size supported_size )

Sets the supported size of this population. It will get reduced to this size through selective pressure.

References supported_size_, and protocols::TR().

Referenced by initialize_from_evotoptions().

◆ size()

core::Size protocols::ligand_evolution::Population::size ( ) const

Returns the size of this population.

References individuals_.

Referenced by add_individuals(), protocols::ligand_evolution::ElitistSelector::apply(), protocols::ligand_evolution::RouletteSelector::apply(), protocols::ligand_evolution::TournamentSelector::apply(), protocols::ligand_evolution::EvolutionManager::calculate_quantiles(), log_generation(), next_generation(), remove_individuals(), and protocols::ligand_evolution::Scorer::score_population().

◆ sort()

void protocols::ligand_evolution::Population::sort ( )

Sorts all individuals depending on their score.

References core::pose::motif::a(), protocols::match::upstream::b, individuals_, is_sorted(), and sorting_guaranteed_.

Referenced by protocols::ligand_evolution::ElitistSelector::apply(), protocols::ligand_evolution::RouletteSelector::apply(), protocols::ligand_evolution::TournamentSelector::apply(), protocols::ligand_evolution::EvolutionManager::calculate_quantiles(), log_generation(), next_generation(), protocols::ligand_evolution::EvolutionManager::run(), and protocols::ligand_evolution::Scorer::score_population().

Member Data Documentation

◆ generation_

core::Size protocols::ligand_evolution::Population::generation_ = 0

private

Referenced by generation(), and next_generation().

◆ generation_log_

utility::vector1< utility::vector1< core::Size > > protocols::ligand_evolution::Population::generation_log_

private

Referenced by expose_generation_log(), and log_generation().

◆ individuals_

utility::vector1< Individual > protocols::ligand_evolution::Population::individuals_

private

Referenced by add_individual(), check_sorting(), individual(), individuals(), log_generation(), remove_individuals(), replace_population(), size(), and sort().

◆ inheritance_graph_

utility::vector1< std::pair< core::Size, core::Size > > protocols::ligand_evolution::Population::inheritance_graph_

private

For debugging and benchmarking purposes. Each entry represents a node in an inheritance graph First is child, second is the parent. If more than one parent is present, more than one entry is created.

Referenced by expand_inheritance_graph(), and expose_inheritance_graph().

◆ next_id_

core::Size protocols::ligand_evolution::Population::next_id_ = 1

private

Keeps track of the next available and unused id.

Referenced by add_individual().

◆ sorting_guaranteed_

bool protocols::ligand_evolution::Population::sorting_guaranteed_ = false

private

Referenced by add_individual(), check_sorting(), individual(), individuals(), is_sorted(), and sort().

◆ supported_size_

core::Size protocols::ligand_evolution::Population::supported_size_ = 0

private

Referenced by next_generation(), and set_supported_size().

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

src/protocols/ligand_evolution/Population.hh
src/protocols/ligand_evolution/Population.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Population()

◆ ~Population()

Member Function Documentation

◆ add_individual()

◆ add_individuals() [1/2]

◆ add_individuals() [2/2]

◆ add_random()

◆ check_sorting()

◆ expand_inheritance_graph()

◆ expose_generation_log()

◆ expose_inheritance_graph()

◆ generation()

◆ individual() [1/2]

◆ individual() [2/2]

◆ individuals() [1/3]

◆ individuals() [2/3]

◆ individuals() [3/3]

◆ initialize_from_evotoptions()

◆ is_sorted()

◆ log_generation()

◆ next_generation()

◆ remove_individuals()

◆ replace_population()

◆ set_supported_size()

◆ size()

◆ sort()

Member Data Documentation

◆ generation_

◆ generation_log_

◆ individuals_

◆ inheritance_graph_

◆ next_id_

◆ sorting_guaranteed_

◆ supported_size_