#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_
std::mt19937	rng_
GeneticIndividual	template_individual_

Friends
class	EvolutionaryDocking

Detailed Description

Definition at line 23 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 86 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 method setup method

◆ start()

virtual void BALL::GeneticAlgorithm::start ( )

virtual

optimize pool

◆ updatePool()

void BALL::GeneticAlgorithm::updatePool ( )

protected

assign fitness score

◆ EvolutionaryDocking

friend class EvolutionaryDocking

friend

Definition at line 25 of file geneticAlgorithm.h.

Member Data Documentation

◆ conv_start_

int BALL::GeneticAlgorithm::conv_start_

protected

iteration for the first convergence test

Definition at line 171 of file geneticAlgorithm.h.

◆ docking_algorithm_

DockingAlgorithm* BALL::GeneticAlgorithm::docking_algorithm_

protected

Definition at line 177 of file geneticAlgorithm.h.

◆ finished_

bool BALL::GeneticAlgorithm::finished_

protected

true if algorithm has stopped

Definition at line 175 of file geneticAlgorithm.h.

◆ gp_

DockProblem* BALL::GeneticAlgorithm::gp_

protected

assings fitness score to individuals

Definition at line 147 of file geneticAlgorithm.h.

◆ immune_

Size BALL::GeneticAlgorithm::immune_

protected

number of individuals immune to mutation

Definition at line 155 of file geneticAlgorithm.h.

◆ iteration_

Size BALL::GeneticAlgorithm::iteration_

protected

count iterations during optimizaton

Definition at line 163 of file geneticAlgorithm.h.

◆ max_iterations_

Size BALL::GeneticAlgorithm::max_iterations_

protected

number of iterations

Definition at line 151 of file geneticAlgorithm.h.

◆ mutation_rate_

double BALL::GeneticAlgorithm::mutation_rate_

protected

fraction of individuals to be mutated

Definition at line 159 of file geneticAlgorithm.h.

◆ parameters_

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

protected

Definition at line 100 of file geneticAlgorithm.h.

◆ pools_

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

protected

vector of populations

Definition at line 135 of file geneticAlgorithm.h.

◆ population_size_

Size BALL::GeneticAlgorithm::population_size_

protected

size of one population

Definition at line 131 of file geneticAlgorithm.h.

◆ probabilities_

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

protected

probabilities for rank weighting

Definition at line 143 of file geneticAlgorithm.h.

◆ rng_

std::mt19937 BALL::GeneticAlgorithm::rng_

protected

RNG engine

Definition at line 181 of file geneticAlgorithm.h.

◆ selected_

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

protected

vector of selected individuals

Definition at line 139 of file geneticAlgorithm.h.

◆ survivors_

Size BALL::GeneticAlgorithm::survivors_

protected

number of individuals surviving an iteration

Definition at line 167 of file geneticAlgorithm.h.

◆ template_individual_

GeneticIndividual BALL::GeneticAlgorithm::template_individual_

protected

used to initialize new individuals

Definition at line 185 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 Symbol 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_