meshi.energy.hydrogenBond
Class HydrogenBondsEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
          meshi.energy.hydrogenBond.HydrogenBondsEnergy

All Implemented Interfaces:

Attributable, Updateable

public class HydrogenBondsEnergy
extends NonBondedEnergyTerm

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

int	elementEvalCounter
protected HydrogenBondsEnergyElement	energyElement
int	evalCounter
protected HBondList	hBondList
int	maxFilterList
int	maxListSize
private HydrogenBondsParametersList	parametersList

Fields inherited from class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm

distanceMatrix

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

HydrogenBondsEnergy()

HydrogenBondsEnergy(DistanceMatrix distanceMatrix, HydrogenBondsParametersList parametersList, double weight, HBondList hBondList)

HydrogenBondsEnergy(DistanceMatrix distanceMatrix, HydrogenBondsParametersList parametersList, double weight, HBondList hBondList, DistanceList specialDistances)

Method Summary

double	evaluate() Evaluates energy for each distance
void	evaluateAtoms() Describe evaluateAtoms method here.
DistanceMatrix	getDistanceMatrix()
HydrogenBondsParametersList	getParametersList()
HBondList	hBondList()

Methods inherited from class meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm

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

Field Detail

hBondList

protected HBondList hBondList

energyElement

protected HydrogenBondsEnergyElement energyElement

parametersList

private HydrogenBondsParametersList parametersList

evalCounter

public int evalCounter

elementEvalCounter

public int elementEvalCounter

maxListSize

public int maxListSize

maxFilterList

public int maxFilterList

Constructor Detail

HydrogenBondsEnergy

public HydrogenBondsEnergy()

HydrogenBondsEnergy

public HydrogenBondsEnergy(DistanceMatrix distanceMatrix,
                           HydrogenBondsParametersList parametersList,
                           double weight,
                           HBondList hBondList)

HydrogenBondsEnergy

public HydrogenBondsEnergy(DistanceMatrix distanceMatrix,
                           HydrogenBondsParametersList parametersList,
                           double weight,
                           HBondList hBondList,
                           DistanceList specialDistances)

Method Detail

getDistanceMatrix

public final DistanceMatrix getDistanceMatrix()

Returns:

Returns the distanceMatrix.

hBondList

public HBondList hBondList()

getParametersList

public final HydrogenBondsParametersList getParametersList()

Returns:

Returns the parametersList.

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