Acopredictor_ant_cycle_cuda_cuh

Functions
__global__ void	HostToDevice::ant_develop_solution (double *pheromone, int nMovElems, int3 *solutions, int3 *moreSolutions, int nCoords, char *relDirections, char *moreRelDirections, int *contacts, char *hpChain, int lsFreq, double alpha, double beta)
	Launches threads such that each thread executes the work of an ant. More...
__global__ void	HostToDevice::find_best_solution (int *contacts, int nContacts, char *directions, int nMovElems, char *outDirections, int *outBestContact)
	Finds the best solution among those produced by ant_develop_solution. More...
__global__ void	HostToDevice::evaporate_pheromones (double *pheromones, int nMovElems, double evapRate)
	Evaporates pheromones in the pheromone matrix. More...
__global__ void	HostToDevice::deposit_pheromones (double *pheromones, int nMovElems, char *directions, int *contacts, int hCount)
	Deposits pheromones in the pheromone matrix, according the each protein's quality. More...

Detailed Description

Function Documentation

ant_develop_solution()

__global__ void HostToDevice::ant_develop_solution	(	double *	pheromone,
		int	nMovElems,
		int3 *	solutions,
		int3 *	moreSolutions,
		int	nCoords,
		char *	relDirections,
		char *	moreRelDirections,
		int *	contacts,
		char *	hpChain,
		int	lsFreq,
		double	alpha,
		double	beta
	)

Launches threads such that each thread executes the work of an ant.

An ant develops a solution by deciding relative directions, using the pheromone matrix as a guide. The ant is also in charge of performing local search by generating small perturbations on the developed protein, and checking if the perturbed one is better.

Parameters

	pheromone	Matrix of pheromones.
	nMovElems	Number of relative movements per protein conformation (probably equal the number of aminoacids minus 2).
	solutions	Memory region that can hold all protein solutions of all threads.
	moreSolutions	Memory region with same size as solutions. Will be used as temporary storage.
	nCoords	Number of coordinates that a protein has (probably equal the number of aminoacids).
	relDirections	Memory region that can hold all arrays of relative directions, one for each launched thread.
	moreRelDirections	Memory region with same size as relDirections. Will be used as temporary storage.
[out]	contacts	Memory region to which we can store the number of contacts for each protein developed by each thread.
	hpChain	The HP chain of the protein being predicted.
	lsFreq	Local Search Frequency, determines the number of protein perturbations to generate after the ant develops the first protein using the pheromones.
	alpha	Alpha parameter of the ACO algorithm.
	beta	Beta parameter of the ACO algortihm.

deposit_pheromones()

__global__ void HostToDevice::deposit_pheromones	(	double *	pheromones,
		int	nMovElems,
		char *	directions,
		int *	contacts,
		int	hCount
	)

Deposits pheromones in the pheromone matrix, according the each protein's quality.

Parameters

pheromones	Pheromone matrix.
nMovElems	Number of relative directions per protein.
directions	Array containing relative directions for all proteins produced by ant_develop_solution.
contacts	Array of contacts produced by ant_develop_solution.
hCount	Number of H beads within the HP chain of the protein being predicted.

evaporate_pheromones()

__global__ void HostToDevice::evaporate_pheromones	(	double *	pheromones,
		int	nMovElems,
		double	evapRate
	)

Evaporates pheromones in the pheromone matrix.

Parameters

[in,out]	pheromones	Pheromone matrix.
	nMovElems	Number of relative directions per protein.
	evapRate	Rate of evaporation of pheromones. Each pheromone is multiplied by (1-evapRate).

find_best_solution()

__global__ void HostToDevice::find_best_solution	(	int *	contacts,
		int	nContacts,
		char *	directions,
		int	nMovElems,
		char *	outDirections,
		int *	outBestContact
	)

Finds the best solution among those produced by ant_develop_solution.

Parameters

	contacts	Array of contacts produced by ant_develop_solution.
	nContacts	number of contacts in contacts.
	directions	Array containing relative directions for all proteins produced by ant_develop_solution.
	nMovElems	Number of relative directions per protein.
[out]	outDirections	Memory region where we can store the relative directions of the best protein identified.
[out]	outBestContact	Memory region (an integer) to which we can store the number of contacts of the best protein identified.