meshi.energy.pairwiseNonBondedTerms
Class NonBondedEnergyTerm

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

All Implemented Interfaces:

Attributable, Updateable

Direct Known Subclasses:

AbstractPunishAngleEnergy, CoulombElectrostatics, ExcludedVol, ExcludedVol, ExcludedVolOLD, FiniteExcludedVol, HydrogenBondsEnergy, HydrogenBondsPairsEnergy, LennardJones

public abstract class NonBondedEnergyTerm
extends AbstractEnergy

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

protected DistanceMatrix	distanceMatrix
protected NonBondedEnergyElement	energyElement Must be initialized on subclass construction.

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

NonBondedEnergyTerm()

NonBondedEnergyTerm(Updateable[] updateableResources, double weight, DistanceMatrix distanceMatrix)
Creates a new NonBondedEnergyTerm instance.

Method Summary

double	evaluate() Evaluates energy for each distance
void	evaluateAtoms() Describe evaluateAtoms method here.
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

distanceMatrix

protected DistanceMatrix distanceMatrix

energyElement

protected NonBondedEnergyElement energyElement

Must be initialized on subclass construction.

Constructor Detail

NonBondedEnergyTerm

public NonBondedEnergyTerm()

NonBondedEnergyTerm

public NonBondedEnergyTerm(Updateable[] updateableResources,
                           double weight,
                           DistanceMatrix distanceMatrix)

Creates a new NonBondedEnergyTerm instance.

Parameters:

updateableResources - an Object[] value

weight - a double value

distanceMatrix - a DistanceMatrix value

Method Detail

evaluate

public double evaluate()

Evaluates energy for each distance

Specified by:

evaluate in class AbstractEnergy

Returns:

a sum of all energy elements

evaluateAtoms

public void evaluateAtoms()

Describe evaluateAtoms method here.

Specified by:

evaluateAtoms in class AbstractEnergy

test

public void test(TotalEnergy totalEnergy,
                 Atom atom)

Testing of one atom in all energy elements

Specified by:

test in class AbstractEnergy

Parameters:

totalEnergy - a TotalEnergy value

atom - an criminal Atom value