The individual holds all information about a single solution in an evolutionary optimization process. More...

#include <Individual.hh>

Public Member Functions
	Individual (LigandIdentifier const &identifier, utility::vector1< core::Size > const &parent_ids, std::string const &type_of_birth)
	Receives a new pose from the fragment library. More...

	~Individual ()

core::Real	score (std::string const &name) const
	Returns the score for the given string. More...

void	score (std::string const &name, core::Real score)
	Sets the score according to the given string. More...

core::Real	score () const
	Returns the total score used by the evolutionary optimization. More...

void	score (core::Real score)
	Sets the total score used by the evolutionary optimization. More...

bool	is_scored () const
	Returns true only if the individual was scored before. More...

LigandIdentifier const &	identifier () const
	Returns the LigandIdentifier of this solution. More...

bool	id (core::Size id)
	Sets the id for this individual. Returns true if a new id was set. More...

core::Size	id () const
	Returns the id of this individual. More...

std::map< std::string, core::Real > const &	score_terms () const
	Read only access to all raw score terms. More...

utility::vector1< core::Size > const &	parents () const
	Returns this individuals parents ids. More...

std::string const &	type_of_birth () const
	Returns this individuals type of birth. More...

Private Attributes
LigandIdentifier	identifier_
	The LigandIdentifier that describes this Individuals ligand. More...

core::Real	score_ = 0.0
	The total score that is actually used for optimization. More...

std::map< std::string, core::Real >	score_terms_
	Stores different score terms with a string identifier. More...

bool	is_scored_ = false
	Saves if a score was already calculated. More...

core::Size	id_ = 0
	A unique number to be identified later. More...

utility::vector1< core::Size >	parent_ids_
	Stores information about the parents of this individual for later analysis. More...

std::string	type_of_birth_
	A short descriptor of how this individual was created. More...

Detailed Description

The individual holds all information about a single solution in an evolutionary optimization process.

Constructor & Destructor Documentation

◆ Individual()

protocols::ligand_evolution::Individual::Individual	(	LigandIdentifier const &	identifier,
		utility::vector1< core::Size > const &	parent_ids,
		std::string const &	type_of_birth
	)

Receives a new pose from the fragment library.

◆ ~Individual()

protocols::ligand_evolution::Individual::~Individual ( )

default

Member Function Documentation

◆ id() [1/2]

core::Size protocols::ligand_evolution::Individual::id ( ) const

Returns the id of this individual.

References id_.

◆ id() [2/2]

bool protocols::ligand_evolution::Individual::id ( core::Size id )

Sets the id for this individual. Returns true if a new id was set.

References id(), id_, and protocols::TR().

Referenced by protocols::ligand_evolution::Crossover::cross(), protocols::ligand_evolution::Population::expand_inheritance_graph(), id(), protocols::ligand_evolution::Mutator::mutate(), protocols::ligand_evolution::Scorer::score_individual(), and protocols::ligand_evolution::Scorer::score_population().

◆ identifier()

LigandIdentifier const & protocols::ligand_evolution::Individual::identifier ( ) const

Returns the LigandIdentifier of this solution.

References identifier_.

Referenced by protocols::ligand_evolution::Crossover::cross(), protocols::ligand_evolution::Mutator::mutate(), protocols::ligand_evolution::Scorer::score_individual(), and protocols::ligand_evolution::Scorer::score_population().

◆ is_scored()

bool protocols::ligand_evolution::Individual::is_scored ( ) const

Returns true only if the individual was scored before.

References is_scored_.

Referenced by protocols::ligand_evolution::Population::check_sorting().

◆ parents()

utility::vector1< core::Size > const & protocols::ligand_evolution::Individual::parents ( ) const

Returns this individuals parents ids.

References parent_ids_.

Referenced by protocols::ligand_evolution::Population::expand_inheritance_graph().

◆ score() [1/4]

core::Real protocols::ligand_evolution::Individual::score ( ) const

Returns the total score used by the evolutionary optimization.

References is_scored_, and score_.

Referenced by score().

◆ score() [2/4]

void protocols::ligand_evolution::Individual::score ( core::Real score )

Sets the total score used by the evolutionary optimization.

References is_scored_, score(), and score_.

◆ score() [3/4]

core::Real protocols::ligand_evolution::Individual::score ( std::string const & name ) const

Returns the score for the given string.

References is_scored_, and score_terms_.

Referenced by protocols::ligand_evolution::RouletteSelector::apply(), protocols::ligand_evolution::EvolutionManager::calculate_quantiles(), protocols::ligand_evolution::Population::check_sorting(), protocols::ligand_evolution::EvolutionManager::run(), protocols::ligand_evolution::Scorer::score_individual(), and protocols::ligand_evolution::Scorer::score_population().

◆ score() [4/4]

void protocols::ligand_evolution::Individual::score	(	std::string const &	name,
		core::Real	score
	)

Sets the score according to the given string.

References score(), and score_terms_.

◆ score_terms()

std::map< std::string, core::Real > const & protocols::ligand_evolution::Individual::score_terms ( ) const

Read only access to all raw score terms.

References score_terms_.

◆ type_of_birth()

std::string const & protocols::ligand_evolution::Individual::type_of_birth ( ) const

Returns this individuals type of birth.

References type_of_birth_.

Member Data Documentation

◆ id_

core::Size protocols::ligand_evolution::Individual::id_ = 0

private

A unique number to be identified later.

Referenced by id().

◆ identifier_

LigandIdentifier protocols::ligand_evolution::Individual::identifier_

private

The LigandIdentifier that describes this Individuals ligand.

Referenced by identifier().

◆ is_scored_

bool protocols::ligand_evolution::Individual::is_scored_ = false

private

Saves if a score was already calculated.

Referenced by is_scored(), and score().

◆ parent_ids_

utility::vector1< core::Size > protocols::ligand_evolution::Individual::parent_ids_

private

Stores information about the parents of this individual for later analysis.

Referenced by parents().

◆ score_

core::Real protocols::ligand_evolution::Individual::score_ = 0.0

private

The total score that is actually used for optimization.

Referenced by score().

◆ score_terms_

std::map< std::string, core::Real > protocols::ligand_evolution::Individual::score_terms_

private

Stores different score terms with a string identifier.

Referenced by score(), and score_terms().

◆ type_of_birth_

std::string protocols::ligand_evolution::Individual::type_of_birth_

private

A short descriptor of how this individual was created.

Referenced by type_of_birth().

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

src/protocols/ligand_evolution/Individual.hh
src/protocols/ligand_evolution/Individual.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Individual()

◆ ~Individual()

Member Function Documentation

◆ id() [1/2]

◆ id() [2/2]

◆ identifier()

◆ is_scored()

◆ parents()

◆ score() [1/4]

◆ score() [2/4]

◆ score() [3/4]

◆ score() [4/4]

◆ score_terms()

◆ type_of_birth()

Member Data Documentation

◆ id_

◆ identifier_

◆ is_scored_

◆ parent_ids_

◆ score_

◆ score_terms_

◆ type_of_birth_