meshi.energy.hydrogenBondsAngle
Class HbondsPunishHOCAngleEnergy

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

All Implemented Interfaces:

Attributable, Updateable

public class HbondsPunishHOCAngleEnergy
extends AbstractPunishAngleEnergy

Created by IntelliJ IDEA. User: amilev Date: 14/03/2006 Time: 14:43:32 This class punish HydrogenBonds with HOC angles < 150 The energy function is zero when the angle is >=150 or when the distance between the Hydrogen and the Oxygen is bigger then 3.5 A.

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

Fields inherited from class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy

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

HbondsPunishHOCAngleEnergy()

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

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

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

Method Summary

void	setComment() set the comment to be the relavent comment according to the instance
void	setEnergyElement() set the energyElement to point on the relavent instance
void	setEnergyElement(double xMax) set the energyElement to point on the relavent instance
void	setEnergyElement(double xMax, double maxAngle) set the energyElement to point on the relavent instance

Methods inherited from class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy

evaluate, evaluateAtoms, test

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

Constructor Detail

HbondsPunishHOCAngleEnergy

public HbondsPunishHOCAngleEnergy()

HbondsPunishHOCAngleEnergy

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

HbondsPunishHOCAngleEnergy

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

HbondsPunishHOCAngleEnergy

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

Method Detail

setEnergyElement

public void setEnergyElement()

set the energyElement to point on the relavent instance

Specified by:

setEnergyElement in class AbstractPunishAngleEnergy

setEnergyElement

public void setEnergyElement(double xMax)

set the energyElement to point on the relavent instance

Specified by:

setEnergyElement in class AbstractPunishAngleEnergy

setEnergyElement

public void setEnergyElement(double xMax,
                             double maxAngle)

set the energyElement to point on the relavent instance

Specified by:

setEnergyElement in class AbstractPunishAngleEnergy

setComment

public void setComment()

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

Specified by:

setComment in class AbstractPunishAngleEnergy