meshi.energy
Class CooperativeEnergyTerm

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.CooperativeEnergyTerm

All Implemented Interfaces:

Attributable, Updateable

Direct Known Subclasses:

EVRot1BBEnergy, LinearRgEnergy, RgEnergy, SideChainSolvateEnergy, SolvateEnergy, SolvateRot1Energy

public abstract class CooperativeEnergyTerm
extends AbstractEnergy

A super class for those energy terms that operate on the entire protein, or on a specific group of atoms that occur only once. Typical cases are Radius of Gyration, or solvation energies.

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

protected AtomList	atomList The atoms relevent to this energy.
protected double[][]	coordinates
protected DistanceMatrix	dm
double	DX
protected Parameters	parameters
double	relativeDiffTolerance
double	verySmall
java.lang.String	XYZ

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

CooperativeEnergyTerm()

CooperativeEnergyTerm(Updateable[] updateableResources, AtomList atomList, DistanceMatrix dm, Parameters parameters, double weight)

Method Summary

void	test(TotalEnergy totalEnergy, Atom atom) Test the accuracy of deriving the energy function by coordinate number "i".

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, evaluate, evaluateAtoms, 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

dm

protected DistanceMatrix dm

atomList

protected AtomList atomList

The atoms relevent to this energy.

parameters

protected Parameters parameters

coordinates

protected double[][] coordinates

DX

public final double DX

See Also:

Constant Field Values

relativeDiffTolerance

public final double relativeDiffTolerance

See Also:

Constant Field Values

verySmall

public final double verySmall

XYZ

public final java.lang.String XYZ

See Also:

Constant Field Values

Constructor Detail

CooperativeEnergyTerm

public CooperativeEnergyTerm()

CooperativeEnergyTerm

public CooperativeEnergyTerm(Updateable[] updateableResources,
                             AtomList atomList,
                             DistanceMatrix dm,
                             Parameters parameters,
                             double weight)

Method Detail

test

public void test(TotalEnergy totalEnergy,
                 Atom atom)

Test the accuracy of deriving the energy function by coordinate number "i". The analytical derivation is compared to the numerical one.

Specified by:

test in class AbstractEnergy