meshi.energy
Class EnergyElement

java.lang.Object
  meshi.energy.EnergyElement

Direct Known Subclasses:

AlphaAngleEnergyElement, AlphaTorsionEnergyElement, AngleEnergyElement, BondEnergyElement, CompositePropensity2DEnergyElement, CompositePropensityEnergyElement, CylinderEnergyElement, EDMEnergyElement, NonBondedEnergyElement, OutOfPlaneEnergyElement, PlaneEnergyElement, RamachandranEnergyElement, RamachandranSidechainEnergyElement, SimpleInflateEnergyElement, SmoothRotamerLibraryEnergyElement, SymmetryEnergyElement, TemplateEnergyElement, TetherEnergyElement, UnWarpEnergyElement, WarpEnergyElement

public abstract class EnergyElement
extends java.lang.Object

The essence of an energy term - its application to a minimal set of atoms. The energy term is a summation of (typically) many such elements.

Field Summary

protected AtomList	atoms
protected static Fdouble	dFormatSrt
protected static Fdouble	dFormatStd
static double	DX
protected boolean	frozen
static double	relativeDiffTolerance
static double	VERY_SMALL
static java.lang.String	XYZ

Constructor Summary

EnergyElement()

Method Summary

AtomList	atoms()
abstract double	evaluate()
double	evaluateAtoms()
boolean	frozen()
protected abstract void	setAtoms()
void	test(TotalEnergy totalEnergy, Atom atom)
boolean	updateFrozen()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

frozen

protected boolean frozen

atoms

protected AtomList atoms

DX

public static final double DX

See Also:

Constant Field Values

relativeDiffTolerance

public static final double relativeDiffTolerance

See Also:

Constant Field Values

VERY_SMALL

public static final double VERY_SMALL

XYZ

public static final java.lang.String XYZ

See Also:

Constant Field Values

dFormatStd

protected static Fdouble dFormatStd

dFormatSrt

protected static Fdouble dFormatSrt

Constructor Detail

EnergyElement

public EnergyElement()

Method Detail

frozen

public final boolean frozen()

atoms

public final AtomList atoms()

updateFrozen

public boolean updateFrozen()

evaluate

public abstract double evaluate()

evaluateAtoms

public double evaluateAtoms()

setAtoms

protected abstract void setAtoms()

test

public void test(TotalEnergy totalEnergy,
                 Atom atom)