meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Class CooperativePerAtomSumma

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma

All Implemented Interfaces:

Attributable, Updateable

public class CooperativePerAtomSumma
extends AbstractEnergy

Created by IntelliJ IDEA. User: tetyanam Date: 01/06/2009 Time: 12:46:56 To change this template use File | Settings | File Templates.

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

private static AtomCore	atom1
private static AtomCore	atom2
private AtomicPairwisePMFSumma	atomicPairwisePMFSumma
private static double	diff1
private static double	diff2
private static DistanceMatrix	distanceMatrix
private static double	factor
private static double[]	mean
private static double[]	std
private static SummaAttribute	summaAttribute
private static AtomType	type1
private static AtomType	type2

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

CooperativePerAtomSumma(DistanceMatrix distanceMatrix, double weight, CooperativePerAtomSummaParameters parameters, AtomicPairwisePMFSumma atomicPairwisePMFSumma)

Method Summary

double	evaluate() Evaluates the energy term and update the derivatives.
double	evaluate(boolean evaluateAtoms)
void	evaluateAtoms() Evaluates the energy term and devides the energy between the atoms.
void	test(TotalEnergy energy, Atom atom) Looking for one "criminal" atom whose derivation is wrong.
private double	zScore(double curE, double mean, double std)

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

atomicPairwisePMFSumma

private AtomicPairwisePMFSumma atomicPairwisePMFSumma

mean

private static final double[] mean

std

private static final double[] std

distanceMatrix

private static DistanceMatrix distanceMatrix

summaAttribute

private static SummaAttribute summaAttribute

atom1

private static AtomCore atom1

atom2

private static AtomCore atom2

type1

private static AtomType type1

type2

private static AtomType type2

diff1

private static double diff1

diff2

private static double diff2

factor

private static double factor

Constructor Detail

CooperativePerAtomSumma

public CooperativePerAtomSumma(DistanceMatrix distanceMatrix,
                               double weight,
                               CooperativePerAtomSummaParameters parameters,
                               AtomicPairwisePMFSumma atomicPairwisePMFSumma)

Method Detail

evaluate

public double evaluate()

Description copied from class: AbstractEnergy

Evaluates the energy term and update the derivatives.

Specified by:

evaluate 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

evaluate

public double evaluate(boolean evaluateAtoms)

zScore

private double zScore(double curE,
                      double mean,
                      double std)

test

public void test(TotalEnergy energy,
                 Atom atom)

Description copied from class: AbstractEnergy

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

Specified by:

test in class AbstractEnergy