meshi.energy.templateEnergy
Class TemplateEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.templateEnergy.TemplateEnergyElement

public class TemplateEnergyElement
extends EnergyElement

Field Summary

private double	BETA
private double	dEdD
private double	dGdD
private double	dis
private double	disDivaidedByDisPlusEpsilon
private double	disPlusEpsilon
private FreeDistance	distance
private double	energy
private double	EPSILON
private double	g
private double	gDividedByGplusBETA
private Atom	movingAtom
private boolean	on
private double	weight

Fields inherited from class meshi.energy.EnergyElement

atoms, dFormatSrt, dFormatStd, DX, frozen, relativeDiffTolerance, VERY_SMALL, XYZ

Constructor Summary

TemplateEnergyElement(Atom frozenAtom, Atom movingAtom, double weight)

Method Summary

double	evaluate()
void	off()
void	offIfUnhappy(double threshold)
Residue	residue()
protected void	setAtoms()
void	update()

Methods inherited from class meshi.energy.EnergyElement

atoms, evaluateAtoms, frozen, test, updateFrozen

Methods inherited from class java.lang.Object

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

Field Detail

distance

private FreeDistance distance

movingAtom

private Atom movingAtom

weight

private double weight

EPSILON

private double EPSILON

BETA

private double BETA

on

private boolean on

dis

private double dis

disPlusEpsilon

private double disPlusEpsilon

disDivaidedByDisPlusEpsilon

private double disDivaidedByDisPlusEpsilon

g

private double g

dGdD

private double dGdD

energy

private double energy

dEdD

private double dEdD

gDividedByGplusBETA

private double gDividedByGplusBETA

Constructor Detail

TemplateEnergyElement

public TemplateEnergyElement(Atom frozenAtom,
                             Atom movingAtom,
                             double weight)

Method Detail

update

public void update()

evaluate

public double evaluate()

Specified by:

evaluate in class EnergyElement

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement

residue

public Residue residue()

off

public void off()

offIfUnhappy

public void offIfUnhappy(double threshold)