meshi.energy.simpleEnergyTerms.alphaTorsion
Class AlphaTorsionEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
          meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy

All Implemented Interfaces:

Attributable, Updateable

public class AlphaTorsionEnergy
extends SimpleEnergyTerm

This energy limits the alpha torsion (4 consecutive CAs) to be in a specific range. It is also secondary structure sensitive, and the range depends on the residue SS. It operates currently only on HELIX,SHEET secondary structure states, since the COIL,ALL states practically don't have any limitation on the alpha torsion. Important Note: This energy term must be accompanied by an ALPHA-angle energy term. This is because it has a non-continous point at torsion values of -Pi or Pi , and also when one of the 2 angles that make up the torsion is close to 0 or Pi. These discontinuites should not affect normal operation if the ALPHA-angle term is working. On very rare starting condition 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 DistanceMatrix	distanceMatrix
protected TorsionList	torsionList

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

AlphaTorsionEnergy()

AlphaTorsionEnergy(TorsionList torsionList, DistanceMatrix distanceMatrix, AlphaTorsionParametersList 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

torsionList

protected TorsionList torsionList

distanceMatrix

protected DistanceMatrix distanceMatrix

Constructor Detail

AlphaTorsionEnergy

public AlphaTorsionEnergy()

AlphaTorsionEnergy

public AlphaTorsionEnergy(TorsionList torsionList,
                          DistanceMatrix distanceMatrix,
                          AlphaTorsionParametersList 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)