meshi.energy.hydrogenBondsPairs
Class HydrogenBondsPairsEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
          meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement

public class HydrogenBondsPairsEnergyElement
extends NonBondedEnergyElement

Field Summary

private boolean	antiParallel
(package private) BetaParametersList	betaParametersList
private double	deDxHAtom1
private double	deDxHAtom2
private double	deDxOAtom1
private double	deDxOAtom2
private double	deDyHAtom1
private double	deDyHAtom2
private double	deDyOAtom1
private double	deDyOAtom2
private double	deDzHAtom1
private double	deDzHAtom2
private double	deDzOAtom1
private double	deDzOAtom2
(package private) HB_DistanceAttribute	distanceAttributes1
(package private) HB_DistanceAttribute	distanceAttributes2
private double	energy
private double	factor
private boolean	free
private Atom	hAtom1
private Atom	hAtom2
(package private) HelixParametersList	helixParametersList
(package private) Distance	HOelement1
(package private) Distance	HOelement2
(package private) double	hpunish
private Atom	oAtom1
private Atom	oAtom2
(package private) int	ooDistance
(package private) double	punish
private int[]	specialDisArray
(package private) static boolean	toPrint
private double	weight

Fields inherited from class meshi.energy.EnergyElement

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

Constructor Summary

HydrogenBondsPairsEnergyElement()

HydrogenBondsPairsEnergyElement(HelixParametersList helixParametersList, BetaParametersList betaParametersList, double weight, double punish, double hpunish)

HydrogenBondsPairsEnergyElement(HelixParametersList helixParametersList, BetaParametersList betaParametersList, double weight, double punish, double hpunish, int[] specialDisArray, boolean antiParallel)

Method Summary

private boolean	antiParallel(HydrogenBondsPairsParameters parameters)
private boolean	antiParallelshift(int resNum1, int resNum2)
double	evaluate()
void	freeElenet()
Atom	oAtom1()
private boolean	parallel(HydrogenBondsPairsParameters parameters)
private boolean	parallelshift(int resNum1, int resNum2)
void	set(java.lang.Object obj)
protected void	setAtoms()
java.lang.String	toString()
void	updateAtoms()
double	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

Field Detail

toPrint

static boolean toPrint

betaParametersList

BetaParametersList betaParametersList

helixParametersList

HelixParametersList helixParametersList

punish

double punish

hpunish

double hpunish

oAtom1

private Atom oAtom1

hAtom1

private Atom hAtom1

oAtom2

private Atom oAtom2

hAtom2

private Atom hAtom2

weight

private double weight

HOelement1

Distance HOelement1

HOelement2

Distance HOelement2

distanceAttributes1

HB_DistanceAttribute distanceAttributes1

distanceAttributes2

HB_DistanceAttribute distanceAttributes2

deDxOAtom1

private double deDxOAtom1

deDyOAtom1

private double deDyOAtom1

deDzOAtom1

private double deDzOAtom1

deDxOAtom2

private double deDxOAtom2

deDyOAtom2

private double deDyOAtom2

deDzOAtom2

private double deDzOAtom2

deDxHAtom1

private double deDxHAtom1

deDyHAtom1

private double deDyHAtom1

deDzHAtom1

private double deDzHAtom1

deDxHAtom2

private double deDxHAtom2

deDyHAtom2

private double deDyHAtom2

deDzHAtom2

private double deDzHAtom2

energy

private double energy

ooDistance

int ooDistance

free

private boolean free

factor

private double factor

specialDisArray

private int[] specialDisArray

antiParallel

private boolean antiParallel

Constructor Detail

HydrogenBondsPairsEnergyElement

public HydrogenBondsPairsEnergyElement()

HydrogenBondsPairsEnergyElement

public HydrogenBondsPairsEnergyElement(HelixParametersList helixParametersList,
                                       BetaParametersList betaParametersList,
                                       double weight,
                                       double punish,
                                       double hpunish)

HydrogenBondsPairsEnergyElement

public HydrogenBondsPairsEnergyElement(HelixParametersList helixParametersList,
                                       BetaParametersList betaParametersList,
                                       double weight,
                                       double punish,
                                       double hpunish,
                                       int[] specialDisArray,
                                       boolean antiParallel)

Method Detail

oAtom1

public final Atom oAtom1()

set

public void set(java.lang.Object obj)

Specified by:

set in class NonBondedEnergyElement

antiParallel

private boolean antiParallel(HydrogenBondsPairsParameters parameters)

parallel

private boolean parallel(HydrogenBondsPairsParameters parameters)

antiParallelshift

private boolean antiParallelshift(int resNum1,
                                  int resNum2)

parallelshift

private boolean parallelshift(int resNum1,
                              int resNum2)

freeElenet

public void freeElenet()

evaluate

public double evaluate()

Specified by:

evaluate in class EnergyElement

updateEnergy

public double updateEnergy()

updateAtoms

public void updateAtoms()

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object