meshi.applications.prediction.beautify.warpEnergy
Class WarpEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.applications.prediction.beautify.warpEnergy.WarpEnergy

All Implemented Interfaces:

Attributable, Updateable

public class WarpEnergy
extends AbstractEnergy
implements Updateable

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

private static WarpEnergyElementsList

elements

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

WarpEnergy(double weight)

Method Summary

void	add(ResidueAlignment residueAlignment)
void	add(ResidueAlignmentColumn column)
double	evaluate() Evaluates the energy term and update the derivatives.
void	evaluateAtoms() Evaluates the energy term and devides the energy between the atoms.
void	ignoreLoopResidues()
void	ignoreUnhappyResidues(double threshold)
void	test(TotalEnergy totalEnergy, Atom atom) Looking for one "criminal" atom whose derivation is wrong.
void	update()
void	update(int i) Updates the updatable resources.

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, getAttribute, handleMissingParameters, isOn, off, on, toArray, toArray, toArray, toArray, toString

Methods inherited from class java.lang.Object

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

Field Detail

elements

private static WarpEnergyElementsList elements

Constructor Detail

WarpEnergy

public WarpEnergy(double weight)

Method Detail

update

public void update()

update

public void update(int i)

Description copied from class: AbstractEnergy

Updates the updatable resources. For a detailed description of MESHI's treatment of updatable resources see the documentation of TotalEnergy.

Specified by:

update in interface Updateable

Overrides:

update in class AbstractEnergy

ignoreLoopResidues

public void ignoreLoopResidues()

ignoreUnhappyResidues

public void ignoreUnhappyResidues(double threshold)

evaluate

public double evaluate()

Description copied from class: AbstractEnergy

Evaluates the energy term and update the derivatives.

Specified by:

evaluate in class AbstractEnergy

test

public void test(TotalEnergy totalEnergy,
                 Atom atom)

Description copied from class: AbstractEnergy

Looking for one "criminal" atom whose derivation is wrong.

Specified by:

test in class AbstractEnergy

evaluateAtoms

public void evaluateAtoms()

Description copied from class: AbstractEnergy

Evaluates the energy term and devides the energy between the atoms. The energy field of each atom is assigned a value - its contribution to the total energy sum.

Specified by:

evaluateAtoms in class AbstractEnergy

add

public void add(ResidueAlignmentColumn column)

add

public void add(ResidueAlignment residueAlignment)