#include <BALL/DOCKING/GENETICDOCK/geneticAlgorithm.h>

Public Member Functions
	GeneticAlgorithm ()

	GeneticAlgorithm (const GeneticAlgorithm &ga)

	GeneticAlgorithm (DockingAlgorithm docker, DockProblem , int pop_number, int iter, int init, int pop, int surv, double mrate, int save, int citer, double cvalue, int cstart)

virtual	~GeneticAlgorithm ()

virtual GeneticAlgorithm &	operator= (const GeneticAlgorithm &ga)

void	setup (DockProblem *, int pop_number, int iter, int init, int pop, int surv, double mrate, int save, int citer, double cvalue, int cstart)

virtual void	start ()

virtual double	getValue ()

GeneticIndividual *	getIndividual (Index i)

bool	registerParameter (GenericParameter *)

Protected Member Functions
double	calculate (GeneticIndividual *)

void	select (Size)

void	mate ()

void	mutate ()

void	cleanUp ()

void	cleanPool (vector< GeneticIndividual > &pool)

bool	multiDemeCheck ()

void	updatePool ()

Protected Attributes
vector< GenericParameter * >	parameters_

Size	population_size_

std::vector< std::vector< GeneticIndividual > >	pools_

std::vector< std::pair< GeneticIndividual , GeneticIndividual > >	selected_

std::vector< double >	probabilities_

DockProblem *	gp_

Size	max_iterations_

Size	immune_

double	mutation_rate_

Size	iteration_

Size	survivors_

int	conv_start_

bool	finished_

DockingAlgorithm *	docking_algorithm_

RandomNumberGenerator	rng_

GeneticIndividual	template_individual_

Friends
class	EvolutionaryDocking

Detailed Description

Definition at line 21 of file geneticAlgorithm.h.

Constructor & Destructor Documentation

§ GeneticAlgorithm() [1/3]

BALL::GeneticAlgorithm::GeneticAlgorithm ( )

default constructor

§ GeneticAlgorithm() [2/3]

BALL::GeneticAlgorithm::GeneticAlgorithm ( const GeneticAlgorithm & ga )

copy constructor

§ GeneticAlgorithm() [3/3]

BALL::GeneticAlgorithm::GeneticAlgorithm	(	DockingAlgorithm *	docker,
		DockProblem *	,
		int	pop_number,
		int	iter,
		int	init,
		int	pop,
		int	surv,
		double	mrate,
		int	save,
		int	citer,
		double	cvalue,
		int	cstart
	)

constructor

§ ~GeneticAlgorithm()

virtual BALL::GeneticAlgorithm::~GeneticAlgorithm ( )

virtual

default destructor

Member Function Documentation

§ calculate()

double BALL::GeneticAlgorithm::calculate ( GeneticIndividual * )

protected

§ cleanPool()

void BALL::GeneticAlgorithm::cleanPool ( vector< GeneticIndividual > & pool )

protected

sorts the given pool according to the fitness values of its members and keeps only the best survivors_>ones (#best ones = survivors_)

§ cleanUp()

void BALL::GeneticAlgorithm::cleanUp ( )

protected

discard individuals

§ getIndividual()

GeneticIndividual* BALL::GeneticAlgorithm::getIndividual ( Index i )

get i-th individual?!?!?

§ getValue()

virtual double BALL::GeneticAlgorithm::getValue ( )

inlinevirtual

Definition at line 83 of file geneticAlgorithm.h.

§ mate()

void BALL::GeneticAlgorithm::mate ( )

protected

produce offsprings

§ multiDemeCheck()

bool BALL::GeneticAlgorithm::multiDemeCheck ( )

protected

check for migration between populations

§ mutate()

void BALL::GeneticAlgorithm::mutate ( )

protected

random alteration

§ operator=()

virtual GeneticAlgorithm& BALL::GeneticAlgorithm::operator= ( const GeneticAlgorithm & ga )

virtual

assignment operator

§ registerParameter()

bool BALL::GeneticAlgorithm::registerParameter ( GenericParameter * )

register a parameter for optimization

§ select()

void BALL::GeneticAlgorithm::select ( Size )

protected

select individuals for mating

§ setup()

void BALL::GeneticAlgorithm::setup	(	DockProblem *	,
		int	pop_number,
		int	iter,
		int	init,
		int	pop,
		int	surv,
		double	mrate,
		int	save,
		int	citer,
		double	cvalue,
		int	cstart
	)

clone methodsetup method

§ start()

virtual void BALL::GeneticAlgorithm::start ( )

virtual

optimize pool

§ updatePool()

void BALL::GeneticAlgorithm::updatePool ( )

protected

assign fitness score

Friends And Related Function Documentation

§ EvolutionaryDocking

friend class EvolutionaryDocking

friend

Definition at line 24 of file geneticAlgorithm.h.

Member Data Documentation

§ conv_start_

int BALL::GeneticAlgorithm::conv_start_

protected

iteration for the first convergence test

Definition at line 168 of file geneticAlgorithm.h.

§ docking_algorithm_

DockingAlgorithm* BALL::GeneticAlgorithm::docking_algorithm_

protected

Definition at line 174 of file geneticAlgorithm.h.

§ finished_

bool BALL::GeneticAlgorithm::finished_

protected

true if algorithm has stopped

Definition at line 172 of file geneticAlgorithm.h.

§ gp_

DockProblem* BALL::GeneticAlgorithm::gp_

protected

assings fitness score to individuals

Definition at line 144 of file geneticAlgorithm.h.

§ immune_

Size BALL::GeneticAlgorithm::immune_

protected

number of individuals immune to mutation

Definition at line 152 of file geneticAlgorithm.h.

§ iteration_

Size BALL::GeneticAlgorithm::iteration_

protected

count iterations during optimizaton

Definition at line 160 of file geneticAlgorithm.h.

§ max_iterations_

Size BALL::GeneticAlgorithm::max_iterations_

protected

number of iterations

Definition at line 148 of file geneticAlgorithm.h.

§ mutation_rate_

double BALL::GeneticAlgorithm::mutation_rate_

protected

fraction of individuals to be mutated

Definition at line 156 of file geneticAlgorithm.h.

§ parameters_

vector<GenericParameter*> BALL::GeneticAlgorithm::parameters_

protected

Definition at line 97 of file geneticAlgorithm.h.

§ pools_

std::vector<std::vector<GeneticIndividual> > BALL::GeneticAlgorithm::pools_

protected

vector of populations

Definition at line 132 of file geneticAlgorithm.h.

§ population_size_

Size BALL::GeneticAlgorithm::population_size_

protected

size of one population

Definition at line 128 of file geneticAlgorithm.h.

§ probabilities_

std::vector<double> BALL::GeneticAlgorithm::probabilities_

protected

probabilities for rank weighting

Definition at line 140 of file geneticAlgorithm.h.

§ rng_

RandomNumberGenerator BALL::GeneticAlgorithm::rng_

protected

Definition at line 178 of file geneticAlgorithm.h.

§ selected_

std::vector<std::pair<GeneticIndividual*, GeneticIndividual*> > BALL::GeneticAlgorithm::selected_

protected

vector of selected individuals

Definition at line 136 of file geneticAlgorithm.h.

§ survivors_

Size BALL::GeneticAlgorithm::survivors_

protected

number of individuals surviving an iteration

Definition at line 164 of file geneticAlgorithm.h.

§ template_individual_

GeneticIndividual BALL::GeneticAlgorithm::template_individual_

protected

used to initialize new individuals

Definition at line 182 of file geneticAlgorithm.h.

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

§ GeneticAlgorithm() [1/3]

§ GeneticAlgorithm() [2/3]

§ GeneticAlgorithm() [3/3]

§ ~GeneticAlgorithm()

Member Function Documentation

§ calculate()

§ cleanPool()

§ cleanUp()

§ getIndividual()

§ getValue()

§ mate()

§ multiDemeCheck()

§ mutate()

§ operator=()

§ registerParameter()

§ select()

§ setup()

§ start()

§ updatePool()

Friends And Related Function Documentation

§ EvolutionaryDocking

Member Data Documentation

§ conv_start_

§ docking_algorithm_

§ finished_

§ gp_

§ immune_

§ iteration_

§ max_iterations_

§ mutation_rate_

§ parameters_

§ pools_

§ population_size_

§ probabilities_

§ rng_

§ selected_

§ survivors_

§ template_individual_