meshi.energy.simpleEnergyTerms.alphaAngle
Class AlphaAngleEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
          meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy

All Implemented Interfaces:

Attributable, Updateable

public class AlphaAngleEnergy
extends SimpleEnergyTerm

This class limits the alpha angle (3 consecutive CAs) to be in a specific range. It is also secondary structure sensitive, and the range depends on the residue SS. The range limitiation is done by putting very steep parabolas on both side of the range. Within the range the energy is a constant 0.0 Important Note: This energy term has a non-continous point at angle values of 0 or Pi. These discontinuites should not normally affect normal operation if the weight set to this term is sufficiently high (of the order of 1-10).On very rare starting condition, however, these problems might never the less be encountered.

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

protected AngleList	angleList
protected DistanceMatrix	distanceMatrix

Fields inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

elementsList, parametersList

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

AlphaAngleEnergy()

AlphaAngleEnergy(AngleList angleList, DistanceMatrix distanceMatrix, AlphaAngleParametersList parametersList, double weight)

Method Summary

EnergyElement	createElement(java.lang.Object baseElement, Parameters parameters)
void	handleMissingParameters(java.lang.Object obj)
void	removeBadBonds(double farAway)

Methods inherited from class meshi.energy.simpleEnergyTerms.SimpleEnergyTerm

createElementsList, elementsList, evaluate, evaluateAtoms, test

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, getAttribute, 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

angleList

protected AngleList angleList

distanceMatrix

protected DistanceMatrix distanceMatrix

Constructor Detail

AlphaAngleEnergy

public AlphaAngleEnergy()

AlphaAngleEnergy

public AlphaAngleEnergy(AngleList angleList,
                        DistanceMatrix distanceMatrix,
                        AlphaAngleParametersList parametersList,
                        double weight)

Method Detail

createElement

public EnergyElement createElement(java.lang.Object baseElement,
                                   Parameters parameters)

Specified by:

createElement in class SimpleEnergyTerm

handleMissingParameters

public void handleMissingParameters(java.lang.Object obj)

Overrides:

handleMissingParameters in class AbstractEnergy

removeBadBonds

public void removeBadBonds(double farAway)