meshi.energy.hydrogenBondsPairs
Class HydrogenBondsPairsEnergy

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

All Implemented Interfaces:

Attributable, Updateable

public class HydrogenBondsPairsEnergy
extends NonBondedEnergyTerm

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

BetaParametersList	betaParametersList
private static double	DIFULT_HPUNISHMENT
private static double	DIFULT_PUNISHMENT
int	elementEvalCounter
int	evalCounter
HelixParametersList	helixParametersList
int	maxFilterListSize
int	maxListSize
protected PairsOfHBEElementsList	pairsOfHBEElementsList

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

HydrogenBondsPairsEnergy()

HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix, HelixParametersList helixParametersList, BetaParametersList betaParametersList, PairsOfHBEElementsList pairsOfHBEElementsList, double weight)

HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix, HelixParametersList helixParametersList, BetaParametersList betaParametersList, PairsOfHBEElementsList pairsOfHBEElementsList, double weight, double punish, double hpunish)

HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix, HelixParametersList helixParametersList, BetaParametersList betaParametersList, PairsOfHBEElementsList pairsOfHBEElementsList, double weight, double punish, double hpunish, int[] specialDisArray, boolean antiParallel)

HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix, HelixParametersList helixParametersList, BetaParametersList betaParametersList, PairsOfHBEElementsList pairsOfHBEElementsList, double weight, int[] specialDisArray, boolean antiParallel)

Method Summary

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

pairsOfHBEElementsList

protected PairsOfHBEElementsList pairsOfHBEElementsList

DIFULT_PUNISHMENT

private static final double DIFULT_PUNISHMENT

See Also:

Constant Field Values

DIFULT_HPUNISHMENT

private static final double DIFULT_HPUNISHMENT

See Also:

Constant Field Values

evalCounter

public int evalCounter

elementEvalCounter

public int elementEvalCounter

maxListSize

public int maxListSize

maxFilterListSize

public int maxFilterListSize

helixParametersList

public HelixParametersList helixParametersList

betaParametersList

public BetaParametersList betaParametersList

Constructor Detail

HydrogenBondsPairsEnergy

public HydrogenBondsPairsEnergy()

HydrogenBondsPairsEnergy

public HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix,
                                HelixParametersList helixParametersList,
                                BetaParametersList betaParametersList,
                                PairsOfHBEElementsList pairsOfHBEElementsList,
                                double weight)

HydrogenBondsPairsEnergy

public HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix,
                                HelixParametersList helixParametersList,
                                BetaParametersList betaParametersList,
                                PairsOfHBEElementsList pairsOfHBEElementsList,
                                double weight,
                                int[] specialDisArray,
                                boolean antiParallel)

HydrogenBondsPairsEnergy

public HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix,
                                HelixParametersList helixParametersList,
                                BetaParametersList betaParametersList,
                                PairsOfHBEElementsList pairsOfHBEElementsList,
                                double weight,
                                double punish,
                                double hpunish)

HydrogenBondsPairsEnergy

public HydrogenBondsPairsEnergy(DistanceMatrix distanceMatrix,
                                HelixParametersList helixParametersList,
                                BetaParametersList betaParametersList,
                                PairsOfHBEElementsList pairsOfHBEElementsList,
                                double weight,
                                double punish,
                                double hpunish,
                                int[] specialDisArray,
                                boolean antiParallel)

Method Detail

getPairsOfHBEElementsList

public PairsOfHBEElementsList getPairsOfHBEElementsList()

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