meshi.energy
Class TotalEnergy

java.lang.Object
  meshi.energy.TotalEnergy

public class TotalEnergy
extends java.lang.Object

A generic class for all meshi energy functions. Typically only a single such object exists, which include several energy term objects (sub classes of AbstractEnergy).

Nested Class Summary

static class	TotalEnergy.EnergyComparator
private static class	TotalEnergy.FreeAtom
private static class	TotalEnergy.IsEnergy
private class	TotalEnergy.SortedAtoms

Field Summary

protected AtomList	atomList
protected static double[][]	coordinates
protected Fdouble	dformat
protected DistanceMatrix	distanceMatrix
(package private) static double	DX
protected java.util.ArrayList<AbstractEnergy>	energyTerms
protected java.util.ArrayList<java.lang.Double>	energyValues
protected Fint	iformat
private static double	INFINITY
protected int	numberOfEvaluations Number of times the energy function was evaluated.
protected int	numberOfReports
protected static int	numberOfUpdates
protected Format	sformat
static Terminator	terminator
private static TotalEnergy	theOnlyTotalEnergy
protected double	totalEnergy
(package private) static double	verySmall
(package private) static java.lang.String[]	XYZ

Constructor Summary

TotalEnergy(AtomList atomList)

TotalEnergy(AtomList atomList, DistanceMatrix distanceMatrix)

TotalEnergy(AtomList atomList, DistanceMatrix distanceMatrix, AbstractEnergy[] energyTerms)

TotalEnergy(Protein protein, DistanceMatrix distanceMatrix, EnergyCreator[] energyCreators, CommandList commands)

TotalEnergy(Protein protein, DistanceMatrix distanceMatrix, EnergyCreator[] energyCreators, CommandList commands, AtomList atoms)

Method Summary

void	add(TotalEnergy energy)
void	addTerm(AbstractEnergy term)
AtomList	atomList()
double	avgEnergy()
double	avgFilteredEnergy(double stdThreshold)
double[][]	coordinates()
DistanceMatrix	distanceMatrix()
double	energy()
java.util.ArrayList<AbstractEnergy>	energyTerms()
java.util.ArrayList<java.lang.Double>	energyValues()
double	evaluate()
void	evaluateAtoms()
double	filteredEnergy(double stdThreshold)
protected Atom	findCriminalAtom() Searching for a `criminal' atom
protected AbstractEnergy	findCriminalEnergyTerm(Atom atom) Searching for a `criminal' energy term , with specific atom
boolean	frozenAtomsExist()
static double	getAverageForce(double[][] coordinates)
void	getCoordinates()
static double[][]	getCoordinates(AtomList atomList) Reduce the Atom coordinates of an atom list to an array.
DistanceMatrix	getDistanceMatrix()
AbstractEnergy	getEnergyTerm(AbstractEnergy ae)
AbstractEnergy[]	getEnergyTerms(AbstractEnergy ae)
double	getGradMagnitude() Finds the maximal component (in magnitude) of the gradient vecor in coordinates ( coordinates[][1] ).
double	getLastEnergy() Returns the last enrgy value that was calculated
AtomList	highestEnergyAtoms(double stdThreshold)
int	numberOfEvaluations()
int	numberOfUpdates()
void	off()
void	on()
java.lang.String	report(int step)
java.lang.String	reportHeader()
void	reset()
void	resetAtomEnergies()
static void	resetForces()
static void	resetForces(double[][] coordinates) Sets all forces to zero.
void	setCoordinates(AtomList atomList)
void	summary()
void	test()
double	totalEnergy()
void	update() Updates all factors related to the energy function (for example the distance matrix).
void	updateDebug()

Methods inherited from class java.lang.Object

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

Field Detail

numberOfEvaluations

protected int numberOfEvaluations

Number of times the energy function was evaluated. This is a simple machine-independent measure of convergence efficiency.

numberOfUpdates

protected static int numberOfUpdates

numberOfReports

protected int numberOfReports

atomList

protected AtomList atomList

coordinates

protected static double[][] coordinates

energyTerms

protected java.util.ArrayList<AbstractEnergy> energyTerms

energyValues

protected java.util.ArrayList<java.lang.Double> energyValues

totalEnergy

protected double totalEnergy

dformat

protected Fdouble dformat

sformat

protected Format sformat

iformat

protected Fint iformat

distanceMatrix

protected DistanceMatrix distanceMatrix

theOnlyTotalEnergy

private static TotalEnergy theOnlyTotalEnergy

terminator

public static final Terminator terminator

INFINITY

private static final double INFINITY

See Also:

Constant Field Values

DX

static final double DX

See Also:

Constant Field Values

XYZ

static final java.lang.String[] XYZ

verySmall

static final double verySmall

Constructor Detail

TotalEnergy

public TotalEnergy(AtomList atomList,
                   DistanceMatrix distanceMatrix,
                   AbstractEnergy[] energyTerms)

TotalEnergy

public TotalEnergy(Protein protein,
                   DistanceMatrix distanceMatrix,
                   EnergyCreator[] energyCreators,
                   CommandList commands)

TotalEnergy

public TotalEnergy(AtomList atomList,
                   DistanceMatrix distanceMatrix)

TotalEnergy

public TotalEnergy(AtomList atomList)

TotalEnergy

public TotalEnergy(Protein protein,
                   DistanceMatrix distanceMatrix,
                   EnergyCreator[] energyCreators,
                   CommandList commands,
                   AtomList atoms)

Method Detail

distanceMatrix

public DistanceMatrix distanceMatrix()

reset

public void reset()

add

public void add(TotalEnergy energy)

test

public void test()

findCriminalAtom

protected Atom findCriminalAtom()

Searching for a `criminal' atom

Returns:

a criminal Atom

findCriminalEnergyTerm

protected AbstractEnergy findCriminalEnergyTerm(Atom atom)

Searching for a `criminal' energy term , with specific atom

Parameters:

atom - a `criminal' Atom

Returns:

a criminal energy term

getGradMagnitude

public double getGradMagnitude()

Finds the maximal component (in magnitude) of the gradient vecor in coordinates ( coordinates[][1] ).

coordinates

public double[][] coordinates()

numberOfEvaluations

public int numberOfEvaluations()

resetForces

public static void resetForces(double[][] coordinates)

Sets all forces to zero.

setCoordinates

public void setCoordinates(AtomList atomList)

getCoordinates

public void getCoordinates()

getCoordinates

public static double[][] getCoordinates(AtomList atomList)

Reduce the Atom coordinates of an atom list to an array. : : : :

evaluateAtoms

public void evaluateAtoms()

evaluate

public double evaluate()

getLastEnergy

public double getLastEnergy()

Returns the last enrgy value that was calculated

update

public void update()
            throws UpdateableException

Updates all factors related to the energy function (for example the distance matrix).

Throws:

UpdateableException

updateDebug

public void updateDebug()

getAverageForce

public static double getAverageForce(double[][] coordinates)

resetForces

public static void resetForces()

reportHeader

public java.lang.String reportHeader()

report

public java.lang.String report(int step)

energy

public double energy()

frozenAtomsExist

public boolean frozenAtomsExist()

atomList

public AtomList atomList()

energyValues

public java.util.ArrayList<java.lang.Double> energyValues()

getEnergyTerm

public AbstractEnergy getEnergyTerm(AbstractEnergy ae)

getDistanceMatrix

public DistanceMatrix getDistanceMatrix()

numberOfUpdates

public final int numberOfUpdates()

addTerm

public void addTerm(AbstractEnergy term)

resetAtomEnergies

public void resetAtomEnergies()

getEnergyTerms

public AbstractEnergy[] getEnergyTerms(AbstractEnergy ae)

totalEnergy

public double totalEnergy()

avgEnergy

public double avgEnergy()

energyTerms

public java.util.ArrayList<AbstractEnergy> energyTerms()

summary

public void summary()

filteredEnergy

public double filteredEnergy(double stdThreshold)

avgFilteredEnergy

public double avgFilteredEnergy(double stdThreshold)

highestEnergyAtoms

public AtomList highestEnergyAtoms(double stdThreshold)

off

public void off()

on

public void on()