BALL::GeneticAlgorithm Class Reference

#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

BALL::GeneticAlgorithm::GeneticAlgorithm

(

)

default constructor

BALL::GeneticAlgorithm::GeneticAlgorithm

(

const GeneticAlgorithm &

ga

)

copy constructor

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

virtual BALL::GeneticAlgorithm::~GeneticAlgorithm ( )

virtual

default destructor

Member Function Documentation

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

protected

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_)

void BALL::GeneticAlgorithm::cleanUp ( )

protected

discard individuals

GeneticIndividual* BALL::GeneticAlgorithm::getIndividual

(

Index

i

)

get i-th individual?!?!?

virtual double BALL::GeneticAlgorithm::getValue ( )

inlinevirtual

Definition at line 83 of file geneticAlgorithm.h.

void BALL::GeneticAlgorithm::mate ( )

protected

produce offsprings

bool BALL::GeneticAlgorithm::multiDemeCheck ( )

protected

check for migration between populations

void BALL::GeneticAlgorithm::mutate ( )

protected

random alteration

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

virtual

assignment operator

bool BALL::GeneticAlgorithm::registerParameter

(

GenericParameter *

)

register a parameter for optimization

void BALL::GeneticAlgorithm::select ( Size  )

protected

select individuals for mating

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

virtual void BALL::GeneticAlgorithm::start ( )

virtual

optimize pool

void BALL::GeneticAlgorithm::updatePool ( )

protected

assign fitness score

Friends And Related Function Documentation

friend class EvolutionaryDocking

friend

Definition at line 24 of file geneticAlgorithm.h.

Member Data Documentation

int BALL::GeneticAlgorithm::conv_start_

protected

iteration for the first convergence test

Definition at line 168 of file geneticAlgorithm.h.

DockingAlgorithm* BALL::GeneticAlgorithm::docking_algorithm_

protected

Definition at line 174 of file geneticAlgorithm.h.

bool BALL::GeneticAlgorithm::finished_

protected

true if algorithm has stopped

Definition at line 172 of file geneticAlgorithm.h.

DockProblem* BALL::GeneticAlgorithm::gp_

protected

assings fitness score to individuals

Definition at line 144 of file geneticAlgorithm.h.

Size BALL::GeneticAlgorithm::immune_

protected

number of individuals immune to mutation

Definition at line 152 of file geneticAlgorithm.h.

Size BALL::GeneticAlgorithm::iteration_

protected

count iterations during optimizaton

Definition at line 160 of file geneticAlgorithm.h.

Size BALL::GeneticAlgorithm::max_iterations_

protected

number of iterations

Definition at line 148 of file geneticAlgorithm.h.

double BALL::GeneticAlgorithm::mutation_rate_

protected

fraction of individuals to be mutated

Definition at line 156 of file geneticAlgorithm.h.

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

protected

Definition at line 97 of file geneticAlgorithm.h.

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

protected

vector of populations

Definition at line 132 of file geneticAlgorithm.h.

Size BALL::GeneticAlgorithm::population_size_

protected

size of one population

Definition at line 128 of file geneticAlgorithm.h.

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

protected

probabilities for rank weighting

Definition at line 140 of file geneticAlgorithm.h.

RandomNumberGenerator BALL::GeneticAlgorithm::rng_

protected

Definition at line 178 of file geneticAlgorithm.h.

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

protected

vector of selected individuals

Definition at line 136 of file geneticAlgorithm.h.

Size BALL::GeneticAlgorithm::survivors_

protected

number of individuals surviving an iteration

Definition at line 164 of file geneticAlgorithm.h.

GeneticIndividual BALL::GeneticAlgorithm::template_individual_

protected

used to initialize new individuals

Definition at line 182 of file geneticAlgorithm.h.