Package ffx.algorithms.optimize.manybody

Class RotamerMatrixMC

java.lang.Object

ffx.algorithms.mc.BoltzmannMC

ffx.algorithms.optimize.manybody.RotamerMatrixMC

All Implemented Interfaces:

MetropolisMC

public class RotamerMatrixMC
extends BoltzmannMC

Monte Carlo driver for DEE-MC.

Field Summary

Fields inherited from class ffx.algorithms.mc.BoltzmannMC

random

Constructor Summary

Constructors

Constructor	Description
RotamerMatrixMC(int[] rotamers, Residue[] residues, boolean useFullAMOEBAEnergy, RotamerOptimization rotamerOptimization)	The Rotamers array must be the same array as passed to any MCMove objects used (and not a copy).

Method Summary

Modifier and Type	Method	Description
protected double	currentEnergy()	If useFullAMOEBAEnergy is set to true, explicitly evaluates energy, else computes energy from the rotamer energy matrices.
void	revertStep()	If possible, reverts the last successful Monte Carlo step taken.
protected void	storeState()	Store the state for reverting a move.

Methods inherited from class ffx.algorithms.mc.BoltzmannMC

acceptChance, evaluateMove, evaluateMove, getAccept, getE1, getE2, getTemperature, lastEnergy, mcStep, mcStep, mcStep, mcStep, setPrint, setRandomSeed, setTemperature

Methods inherited from class java.lang.Object

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

Constructor Details

RotamerMatrixMC

public RotamerMatrixMC(int[] rotamers,
 Residue[] residues,
 boolean useFullAMOEBAEnergy,
 RotamerOptimization rotamerOptimization)

The Rotamers array must be the same array as passed to any MCMove objects used (and not a copy).

Parameters:

rotamers - Array of rotamers.

residues - Array of residues.

useFullAMOEBAEnergy - If true, re-evaluate AMOEBA energy for each conformation.

rotamerOptimization - RotamerOptimization instance.

Method Details

revertStep

public void revertStep()

Description copied from interface: MetropolisMC

If possible, reverts the last successful Monte Carlo step taken.

currentEnergy

protected double currentEnergy()

If useFullAMOEBAEnergy is set to true, explicitly evaluates energy, else computes energy from the rotamer energy matrices.

Specified by:

currentEnergy in class BoltzmannMC

Returns:

Energy at the current state

storeState

protected void storeState()

Description copied from class: BoltzmannMC

Store the state for reverting a move. Must be properly implemented for revertStep() to function properly; otherwise, the implementation of revertStep() should throw an OperationNotSupportedException.

Specified by:

storeState in class BoltzmannMC