Class StandardProteinFoldingProvider

java.lang.Object

org.episteme.natural.biology.structure.providers.StandardProteinFoldingProvider

All Implemented Interfaces:

AlgorithmProvider, ProteinFoldingProvider

public class StandardProteinFoldingProvider
extends Object
implements ProteinFoldingProvider

Standard implementation of HP model folding.

Constructor Summary

Constructors

Constructor	Description
StandardProteinFoldingProvider()

Method Summary

Modifier and Type	Method	Description
Real	calculateEnergy(int[][] positions, boolean[] isH)	Calculates energy for a fold.
double	calculateEnergyDouble(int[][] positions, boolean[] isH)
float	calculateEnergyFloat(int[][] positions, boolean[] isH)
String	getAlgorithmType()	Returns the unique category of the algorithm.
String	getName()
void	simulate(int[][] pos, boolean[] isH, int iterations, double temp, long seed)	Performs Monte-Carlo steps.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface AlgorithmProvider

description, getMetadata, getPriority, isAvailable, score, shutdown

Constructor Details

StandardProteinFoldingProvider

public StandardProteinFoldingProvider()

Method Details

calculateEnergy

public Real calculateEnergy(int[][] positions,
 boolean[] isH)

Description copied from interface: ProteinFoldingProvider

Calculates energy for a fold.

Specified by:

calculateEnergy in interface ProteinFoldingProvider

calculateEnergyDouble

public double calculateEnergyDouble(int[][] positions,
 boolean[] isH)

Specified by:

calculateEnergyDouble in interface ProteinFoldingProvider

calculateEnergyFloat

public float calculateEnergyFloat(int[][] positions,
 boolean[] isH)

Specified by:

calculateEnergyFloat in interface ProteinFoldingProvider

simulate

public void simulate(int[][] pos,
 boolean[] isH,
 int iterations,
 double temp,
 long seed)

Description copied from interface: ProteinFoldingProvider

Performs Monte-Carlo steps.

Specified by:

simulate in interface ProteinFoldingProvider

getName

public String getName()

Specified by:

getName in interface AlgorithmProvider

getAlgorithmType

public String getAlgorithmType()

Description copied from interface: AlgorithmProvider

Returns the unique category of the algorithm.

Specified by:

getAlgorithmType in interface AlgorithmProvider