meshi.energy.hydrogenBond
Class HydrogenBondsEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.hydrogenBond.HydrogenBondsEnergyElement

public class HydrogenBondsEnergyElement
extends NonBondedEnergyElement

Field Summary

static double	ALPHA
private Atom	atom1
private Atom	atom2
private double	contact
private double	dCdD
private double	dEdD
private double	dEdX
private double	deDxHAtom
private double	deDxOAtom
private double	dEdY
private double	deDyHAtom
private double	deDyOAtom
private double	dEdZ
private double	deDzHAtom
private double	deDzOAtom
private Distance	distance
private double	energy
private double	epsilon
private boolean	free
protected Atom	hAtom
HB_DistanceAttribute	hb_Attribute
private int	hFactor
private double	minusTwelveSigma6
protected Atom	oAtom
private int	oFactor
private static double	ONE_DIV_SIX
private double	rMax
private double	sigma
private double	sigma6
private double	sigma6EpsilonFour
private static double	SQR_SIX_OF_TWO
private double	sqrSixOfTwoSigma
private double	weight

Fields inherited from class meshi.energy.EnergyElement

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

Constructor Summary

HydrogenBondsEnergyElement()

HydrogenBondsEnergyElement(double weight)

Method Summary

double	deDxHAtom()
double	deDxOAtom()
double	deDyHAtom()
double	deDyOAtom()
double	deDzHAtom()
double	deDzOAtom()
double	distanceValue()
double	energy()
double	evaluate()
double	evaluate(double weight)
void	freeElement()
Atom	hAtom()
Atom	oAtom()
void	set(java.lang.Object obj)
protected void	setAtoms()
java.lang.String	toString()
private void	updateAtoms()
private void	updateAtoms(double weight)
double	updateEnergy() energy and dirivarives calculation.

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, wait, wait, wait

Field Detail

weight

private double weight

energy

private double energy

oAtom

protected Atom oAtom

hAtom

protected Atom hAtom

deDxOAtom

private double deDxOAtom

deDyOAtom

private double deDyOAtom

deDzOAtom

private double deDzOAtom

deDxHAtom

private double deDxHAtom

deDyHAtom

private double deDyHAtom

deDzHAtom

private double deDzHAtom

dEdD

private double dEdD

dEdX

private double dEdX

dEdY

private double dEdY

dEdZ

private double dEdZ

hFactor

private int hFactor

oFactor

private int oFactor

ALPHA

public static final double ALPHA

See Also:

Constant Field Values

ONE_DIV_SIX

private static final double ONE_DIV_SIX

See Also:

Constant Field Values

SQR_SIX_OF_TWO

private static final double SQR_SIX_OF_TWO

rMax

private double rMax

epsilon

private double epsilon

sigma

private double sigma

sigma6

private double sigma6

sigma6EpsilonFour

private double sigma6EpsilonFour

minusTwelveSigma6

private double minusTwelveSigma6

atom1

private Atom atom1

atom2

private Atom atom2

contact

private double contact

dCdD

private double dCdD

free

private boolean free

sqrSixOfTwoSigma

private double sqrSixOfTwoSigma

distance

private Distance distance

hb_Attribute

public HB_DistanceAttribute hb_Attribute

Constructor Detail

HydrogenBondsEnergyElement

public HydrogenBondsEnergyElement()

HydrogenBondsEnergyElement

public HydrogenBondsEnergyElement(double weight)

Method Detail

set

public void set(java.lang.Object obj)

Specified by:

set in class NonBondedEnergyElement

evaluate

public double evaluate(double weight)

evaluate

public double evaluate()

Specified by:

evaluate in class EnergyElement

freeElement

public void freeElement()

updateEnergy

public double updateEnergy()

energy and dirivarives calculation.

updateAtoms

private void updateAtoms()

updateAtoms

private void updateAtoms(double weight)

deDxOAtom

public final double deDxOAtom()

deDyOAtom

public final double deDyOAtom()

deDzOAtom

public final double deDzOAtom()

deDxHAtom

public final double deDxHAtom()

deDyHAtom

public final double deDyHAtom()

deDzHAtom

public final double deDzHAtom()

energy

public final double energy()

oAtom

public final Atom oAtom()

hAtom

public final Atom hAtom()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

distanceValue

public final double distanceValue()

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement