meshi.energy.solvateRot1
Class SolvateRot1Energy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.CooperativeEnergyTerm
          meshi.energy.solvateRot1.SolvateRot1Energy

All Implemented Interfaces:

Attributable, Rot1Arrays, Updateable

public final class SolvateRot1Energy
extends CooperativeEnergyTerm
implements Rot1Arrays

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

private int	atomListSize
private double[]	AtomSumSigmC
private double[]	dAtomEnergydEnvior
private double[]	dSplineVals
private double[]	forceX
private double[]	forceY
private double[]	forceZ
private int[]	lut These fields are for general use in the class
private double	maximalZ
private double[][]	means
private double[][]	oneOverSTDs
private SolvateRot1ParametersList	parameters
private double[]	residueVals These are fields for temporary array results that are needed in the evaluation stage.
private Spline1D[]	splines
private double[]	splineVals

Fields inherited from class meshi.energy.CooperativeEnergyTerm

atomList, coordinates, dm, DX, relativeDiffTolerance, verySmall, XYZ

Fields inherited from class meshi.energy.AbstractEnergy

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

Fields inherited from interface meshi.util.rotamericTools.Rot1Arrays

mean, std

Constructor Summary

SolvateRot1Energy()

SolvateRot1Energy(AtomList atomList, DistanceMatrix dm, SolvateRot1ParametersList parameters, double[][] pp, double maximalZ, double weight)

Method Summary

void	calcMeansAndStd(double[][] pp)
double	evaluate() Evaluates the energy term and update the derivatives.
double	evaluate(boolean updateAtoms)
void	evaluateAtoms() Evaluates the energy term and devides the energy between the atoms.
void	setComment(java.lang.String str)
private void	updateSigmVals(Distance dis) Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis.

Methods inherited from class meshi.energy.CooperativeEnergyTerm

test

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, 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

residueVals

private double[] residueVals

These are fields for temporary array results that are needed in the evaluation stage. They are declared as fields so that time will not be waisted on creating new instances of the arrays.

splineVals

private double[] splineVals

dSplineVals

private double[] dSplineVals

AtomSumSigmC

private double[] AtomSumSigmC

dAtomEnergydEnvior

private double[] dAtomEnergydEnvior

forceX

private double[] forceX

forceY

private double[] forceY

forceZ

private double[] forceZ

lut

private int[] lut

These fields are for general use in the class

atomListSize

private int atomListSize

parameters

private SolvateRot1ParametersList parameters

splines

private Spline1D[] splines

means

private double[][] means

oneOverSTDs

private double[][] oneOverSTDs

maximalZ

private double maximalZ

Constructor Detail

SolvateRot1Energy

public SolvateRot1Energy()

SolvateRot1Energy

public SolvateRot1Energy(AtomList atomList,
                         DistanceMatrix dm,
                         SolvateRot1ParametersList parameters,
                         double[][] pp,
                         double maximalZ,
                         double weight)

Method Detail

setComment

public void setComment(java.lang.String str)

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

evaluate

public double evaluate()

Description copied from class: AbstractEnergy

Evaluates the energy term and update the derivatives.

Specified by:

evaluate in class AbstractEnergy

evaluate

public final double evaluate(boolean updateAtoms)

updateSigmVals

private final void updateSigmVals(Distance dis)

Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis. The results are updated in the fields of the SolvateDistanceAttribute of dis - sigmaValues.

calcMeansAndStd

public void calcMeansAndStd(double[][] pp)