meshi.energy.hydrogenBondsAngle
Class AbstractPunishAngleEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
          meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy

All Implemented Interfaces:

Attributable, Updateable

Direct Known Subclasses:

HbondsPunishHOCAngleEnergy, HBondsPunishOHNAngleEnergy

public abstract class AbstractPunishAngleEnergy
extends NonBondedEnergyTerm

Created by IntelliJ IDEA. User: amilev Date: 14/03/2006 Time: 14:13:56 To change this template use File | Settings | File Templates.

Nested Class Summary

Nested classes/interfaces inherited from class meshi.energy.AbstractEnergy

AbstractEnergy.UpdateableList

Field Summary

protected HBondList

hBondList

Fields inherited from class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm

distanceMatrix, energyElement

Fields inherited from class meshi.energy.AbstractEnergy

comment, filter, INFINITY, NaN, on, updateableResources, weight

Constructor Summary

AbstractPunishAngleEnergy()

AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix, HBondList hBondList, double weight)

AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix, HBondList hBondList, double weight, DistanceList specialDis)

AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix, HBondList hBondList, double weight, DistanceList specialDis, double xMAx)

AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix, HBondList hBondList, double weight, DistanceList specialDis, double xMax, double maxAngle)

AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix, HBondList hBondList, double weight, double xMax)

AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix, HBondList hBondList, double weight, double xMax, double maxAngle)

Method Summary

double	evaluate() Evaluates energy for each distance
void	evaluateAtoms() Describe evaluateAtoms method here.
abstract void	setComment() set the comment to be the relavent comment according to the instance
abstract void	setEnergyElement() set the energyElement to point on the relavent instance
abstract void	setEnergyElement(double xMax) set the energyElement to point on the relavent instance
abstract void	setEnergyElement(double xMax, double maxAngle) set the energyElement to point on the relavent instance
void	test(TotalEnergy totalEnergy, Atom atom) Testing of one atom in all energy elements

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, getAttribute, handleMissingParameters, isOn, off, on, toArray, toArray, toArray, toArray, toString, update

Methods inherited from class java.lang.Object

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

Field Detail

hBondList

protected HBondList hBondList

Constructor Detail

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy()

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix,
                                 HBondList hBondList,
                                 double weight)

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix,
                                 HBondList hBondList,
                                 double weight,
                                 double xMax)

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix,
                                 HBondList hBondList,
                                 double weight,
                                 double xMax,
                                 double maxAngle)

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix,
                                 HBondList hBondList,
                                 double weight,
                                 DistanceList specialDis)

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix,
                                 HBondList hBondList,
                                 double weight,
                                 DistanceList specialDis,
                                 double xMAx)

AbstractPunishAngleEnergy

public AbstractPunishAngleEnergy(DistanceMatrix distanceMatrix,
                                 HBondList hBondList,
                                 double weight,
                                 DistanceList specialDis,
                                 double xMax,
                                 double maxAngle)

Method Detail

setEnergyElement

public abstract void setEnergyElement()

set the energyElement to point on the relavent instance

setEnergyElement

public abstract void setEnergyElement(double xMax)

set the energyElement to point on the relavent instance

setEnergyElement

public abstract void setEnergyElement(double xMax,
                                      double maxAngle)

set the energyElement to point on the relavent instance

setComment

public abstract void setComment()

set the comment to be the relavent comment according to the instance

evaluate

public double evaluate()

Description copied from class: NonBondedEnergyTerm

Evaluates energy for each distance

Overrides:

evaluate in class NonBondedEnergyTerm

Returns:

a sum of all energy elements

evaluateAtoms

public void evaluateAtoms()

Description copied from class: NonBondedEnergyTerm

Describe evaluateAtoms method here.

Overrides:

evaluateAtoms in class NonBondedEnergyTerm

test

public void test(TotalEnergy totalEnergy,
                 Atom atom)

Description copied from class: NonBondedEnergyTerm

Testing of one atom in all energy elements

Overrides:

test in class NonBondedEnergyTerm

Parameters:

totalEnergy - a TotalEnergy value

atom - an criminal Atom value