meshi.energy.hydrogenBondsAngle
Class HbondsPunishHOCAngleEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
              meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement

public class HbondsPunishHOCAngleEnergyElement
extends AbstractPunishAngleEnergyElement

Created by IntelliJ IDEA. User: amilev Date: 14/03/2006 Time: 14:31:36 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.

Field Summary

Fields inherited from class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement

a1, a2, angle, angleEnergy, angleValue, angleValue2, atom1, atom2, b1, b2, c1, c2, dAngleEnergyDAngle, dAngleEnergyDxHAtom, dAngleEnergyDxOAtom, dAngleEnergyDxTheidAtom, dAngleEnergyDyHAtom, dAngleEnergyDyOAtom, dAngleEnergyDyTheidAtom, dAngleEnergyDzHAtom, dAngleEnergyDzOAtom, dAngleEnergyDzTheidAtom, dDistanceEnergy_Ddistance, dDistanceEnergyDx, dDistanceEnergyDxHAtom, dDistanceEnergyDxOAtom, dDistanceEnergyDy, dDistanceEnergyDyHAtom, dDistanceEnergyDyOAtom, dDistanceEnergyDz, dDistanceEnergyDzHAtom, dDistanceEnergyDzOAtom, deDxHAtom, deDxOAtom, deDxTheidAtom, deDyHAtom, deDyOAtom, deDyTheidAtom, deDzHAtom, deDzOAtom, deDzTheidAtom, distance, distanceEnergy, distanceMatrix, distanceValue, distanceValue2, energy, hAtom, hFactor, oAtom, oFactor, theirdAtom, weight, X_ANGLE, X_ANGLE2, X_MAX, X_MAX2, y1X_Angle2

Fields inherited from class meshi.energy.EnergyElement

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

Constructor Summary

HbondsPunishHOCAngleEnergyElement(DistanceMatrix distanceMatrix, double weight)

HbondsPunishHOCAngleEnergyElement(DistanceMatrix distanceMatrix, double weight, double xMax)

HbondsPunishHOCAngleEnergyElement(DistanceMatrix distanceMatrix, double weight, double xMax, double maxAngle)

Method Summary

java.lang.String	comment()
boolean	setAngle()
void	setDAngleEnergyDatoms()
void	setTheirdAtom()
java.lang.String	toString()
void	updateTheirdAtom()
void	updateTheirdAtom(double weight)

Methods inherited from class meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement

evaluate, evaluate, set, setAtoms, updateAtoms, updateAtoms, updateEnergy

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

Constructor Detail

HbondsPunishHOCAngleEnergyElement

public HbondsPunishHOCAngleEnergyElement(DistanceMatrix distanceMatrix,
                                         double weight)

HbondsPunishHOCAngleEnergyElement

public HbondsPunishHOCAngleEnergyElement(DistanceMatrix distanceMatrix,
                                         double weight,
                                         double xMax)

HbondsPunishHOCAngleEnergyElement

public HbondsPunishHOCAngleEnergyElement(DistanceMatrix distanceMatrix,
                                         double weight,
                                         double xMax,
                                         double maxAngle)

Method Detail

comment

public java.lang.String comment()

Specified by:

comment in class AbstractPunishAngleEnergyElement

setTheirdAtom

public void setTheirdAtom()

Specified by:

setTheirdAtom in class AbstractPunishAngleEnergyElement

setDAngleEnergyDatoms

public void setDAngleEnergyDatoms()

Specified by:

setDAngleEnergyDatoms in class AbstractPunishAngleEnergyElement

setAngle

public boolean setAngle()

Specified by:

setAngle in class AbstractPunishAngleEnergyElement

updateTheirdAtom

public void updateTheirdAtom()

Specified by:

updateTheirdAtom in class AbstractPunishAngleEnergyElement

updateTheirdAtom

public void updateTheirdAtom(double weight)

Specified by:

updateTheirdAtom in class AbstractPunishAngleEnergyElement

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object