Encapsulates the whole process of performing Ant Colony Optimization to find a protein conformation with low free energy. More...

#include <acopredictor.h>

Classes
struct	Results
	Structures used to return results to the callee. More...

Public Member Functions
	ACOPredictor (const Config &config)
	Constructor from configuration file. More...

	~ACOPredictor ()
	The destructor frees memory allocated for holding internal data structures. More...

struct Results	predict ()
	Runs the ACO optimization to predict the protein structure. More...

Private Member Functions
double &	pheromone (int i, int d) const
	Returns the pheromone at step i and direction d. More...

double	random (int tid=0)
	Returns a random number in [0,1). More...

std::vector< double >	get_heuristics (const std::vector< vec3< int >> &possiblePos, const std::vector< vec3< int >> &beadVector)
	Returns a vector V with 5 heuristics. More...

std::vector< double >	get_probabilities (int movIndex, std::vector< double > heuristics) const
	Return a vector V with 5 probabilities. More...

ACOSolution	ant_develop_solution (int tid=0)
	Makes an ant develop a solution, beginning from the start. More...

void	ant_deposit_pheromone (const std::vector< char > &directions, int nContacts)
	Deposits pheromones along the trail followed by the given ant. More...

void	perform_cycle (std::vector< ACOSolution > &antsSolutions, int *nContacts)
	Performs a cycle of the ant colony. More...

Private Attributes
int	dNMovElems
	Stores the number of moviments performed by an ant; its value is N-2 where N is the number of beads in the protein. More...

int	dHCount
	Stores the number of hydrophobic (H) beads in the protein.

double *	dPheromone
	Pheromone matrix. More...

std::vector< std::mt19937 >	dRandGen
	Random number generators used throughout the ACO algorithm. More...

std::uniform_real_distribution	dRandDist
	Random distribution that uses `dRandGen` to generate random numbers. More...

ACOSolution	dBestSol
	Holds the best solution found by this colony. More...

int	dBestContacts
	Holds the num of contacts in the best solution. More...


HPChain	dHPChain
	See the user configuration file for documentation. More...

int	dCycles
	See the user configuration file for documentation. More...

int	dNAnts
	See the user configuration file for documentation. More...

double	dAlpha
	See the user configuration file for documentation. More...

double	dBeta
	See the user configuration file for documentation. More...

double	dEvap
	See the user configuration file for documentation. More...

int	dLSFreq
	See the user configuration file for documentation. More...

int	dExchangedAnts
	See the user configuration file for documentation. More...

int	dRandSeed
	See the user configuration file for documentation. More...

Detailed Description

Encapsulates the whole process of performing Ant Colony Optimization to find a protein conformation with low free energy.

Constructor & Destructor Documentation

◆ ACOPredictor()

ACOPredictor::ACOPredictor ( const Config & config )

Constructor from configuration file.

Parameters

config The configuration file object from which we can read user configured-parameters.

◆ ~ACOPredictor()

ACOPredictor::~ACOPredictor ( )

The destructor frees memory allocated for holding internal data structures.

Member Function Documentation

◆ ant_deposit_pheromone()

void ACOPredictor::ant_deposit_pheromone	(	const std::vector< char > &	directions,
		int	nContacts
	)

inlineprivate

Deposits pheromones along the trail followed by the given ant.

Parameters

directions	Vector of directions followed by the ant.
nContacts	Number of H-H contacts in the protein built by the given ant.

◆ ant_develop_solution()

ACOSolution ACOPredictor::ant_develop_solution ( int tid = 0 )

private

Makes an ant develop a solution, beginning from the start.

Returns the developed solution.

◆ get_heuristics()

vector< double > ACOPredictor::get_heuristics	(	const std::vector< vec3< int >> &	possiblePos,
		const std::vector< vec3< int >> &	beadVector
	)

private

Returns a vector V with 5 heuristics.

V[d] is the heuristic associated with direction d.

◆ get_probabilities()

vector< double > ACOPredictor::get_probabilities	(	int	movIndex,
		std::vector< double >	heuristics
	)		const

private

Return a vector V with 5 probabilities.

V[d] is the probability of going to direction d.

◆ perform_cycle()

void ACOPredictor::perform_cycle	(	std::vector< ACOSolution > &	antsSolutions,
		int *	nContacts
	)

private

Performs a cycle of the ant colony.

A cycle consitst of each:

ant developing a solution,
calculating the solution contacts,
performing local search in each solution,
finding the best solution generated,
evaporating pheromones and finally
depositing pheromones.

This function is the one parallelized for multiple parallel programming models, in the files acopredictor_ant_cycle[...].

◆ pheromone()

double & ACOPredictor::pheromone	(	int	i,
		int	d
	)		const

inlineprivate

Returns the pheromone at step i and direction d.

◆ predict()

struct ACOPredictor::Results ACOPredictor::predict ( )

Runs the ACO optimization to predict the protein structure.

Returns: the best solution found by the optimization algorithm.

◆ random()

double ACOPredictor::random ( int tid = 0 )

inlineprivate

Returns a random number in [0,1).

Member Data Documentation

◆ dAlpha

double ACOPredictor::dAlpha

private

See the user configuration file for documentation.

◆ dBestContacts

int ACOPredictor::dBestContacts

private

Holds the num of contacts in the best solution.

◆ dBestSol

ACOSolution ACOPredictor::dBestSol

private

Holds the best solution found by this colony.

◆ dBeta

double ACOPredictor::dBeta

private

See the user configuration file for documentation.

◆ dCycles

int ACOPredictor::dCycles

private

See the user configuration file for documentation.

◆ dEvap

double ACOPredictor::dEvap

private

See the user configuration file for documentation.

◆ dExchangedAnts

int ACOPredictor::dExchangedAnts

private

See the user configuration file for documentation.

◆ dHPChain

HPChain ACOPredictor::dHPChain

private

See the user configuration file for documentation.

◆ dLSFreq

int ACOPredictor::dLSFreq

private

See the user configuration file for documentation.

◆ dNAnts

int ACOPredictor::dNAnts

private

See the user configuration file for documentation.

◆ dNMovElems

int ACOPredictor::dNMovElems

private

Stores the number of moviments performed by an ant; its value is N-2 where N is the number of beads in the protein.

◆ dPheromone

double* ACOPredictor::dPheromone

private

Pheromone matrix.

◆ dRandDist

std::uniform_real_distribution ACOPredictor::dRandDist

private

Random distribution that uses dRandGen to generate random numbers.

◆ dRandGen

std::vector<std::mt19937> ACOPredictor::dRandGen

private

Random number generators used throughout the ACO algorithm.

◆ dRandSeed

int ACOPredictor::dRandSeed

private

See the user configuration file for documentation.

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ACOPredictor()

◆ ~ACOPredictor()

Member Function Documentation

◆ ant_deposit_pheromone()

◆ ant_develop_solution()

◆ get_heuristics()

◆ get_probabilities()

◆ perform_cycle()

◆ pheromone()

◆ predict()

◆ random()

Member Data Documentation

◆ dAlpha

◆ dBestContacts

◆ dBestSol

◆ dBeta

◆ dCycles

◆ dEvap

◆ dExchangedAnts

◆ dHPChain

◆ dLSFreq

◆ dNAnts

◆ dNMovElems

◆ dPheromone

◆ dRandDist

◆ dRandGen

◆ dRandSeed