meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Class AtomicPairwisePMFSumma

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

All Implemented Interfaces:

Attributable, Updateable

public class AtomicPairwisePMFSumma
extends AbstractEnergy

Atomic pairwise potential of mean force, original energy term by Chris Summa. Reference: Summa CM and Levitt M, Near-native structure refinement using in vacuo energy minimization. PNAS 2007;104(9):3177-82.

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

private static AtomCore	atom1
static int	atom1TypeOrdinal
private static AtomCore	atom2
static int	atom2TypeOrdinal
static double[]	atomEnergies
static int	atomTypeOrdinal
private static int	bin
private static CoefficientsMatrixForAtomPairSpline	coefs
private static double	d
DistanceMatrix	distanceMatrix
private static double	e
private static double	energy0
private static double	energy1
private boolean	frozenFlag
private static double	fx
private static double	fy
private static double	fz
private static double	halfEnergy0
protected static int[]	numberOfEachAtomType
private static int	numberOfTypes
private AtomicPairwisePMFSummaParameters	parameters
protected static double[]	sm2PerAtomType
private static SummaAttribute	summaAttribute
protected static double[]	sumPerAtomType
private static double	x
private static double	x2
private static double	x3

Fields inherited from class meshi.energy.AbstractEnergy

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

Constructor Summary

AtomicPairwisePMFSumma(DistanceMatrix distanceMatrix, double weight, AtomicPairwisePMFSummaParameters parameters)

Method Summary

double	evaluate() Evaluates energy for each distance
double	evaluate(boolean evaluateAtoms)
void	evaluateAtoms() Describe evaluateAtoms method here.
double	evaluateElement(Distance distance, boolean evaluateAtoms)
static int[]	numberOfEachAtomType()
static double[]	sm2PerAtomType()
static double[]	sumPerAtomType()
void	test(TotalEnergy totalEnergy, Atom atom) Looking for one "criminal" atom whose derivation is wrong.

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

distanceMatrix

public final DistanceMatrix distanceMatrix

frozenFlag

private boolean frozenFlag

atom1

private static AtomCore atom1

atom2

private static AtomCore atom2

bin

private static int bin

d

private static double d

energy0

private static double energy0

energy1

private static double energy1

x

private static double x

x2

private static double x2

x3

private static double x3

fx

private static double fx

fy

private static double fy

fz

private static double fz

halfEnergy0

private static double halfEnergy0

e

private static double e

coefs

private static CoefficientsMatrixForAtomPairSpline coefs

numberOfTypes

private static int numberOfTypes

parameters

private AtomicPairwisePMFSummaParameters parameters

sumPerAtomType

protected static final double[] sumPerAtomType

sm2PerAtomType

protected static final double[] sm2PerAtomType

numberOfEachAtomType

protected static int[] numberOfEachAtomType

atom1TypeOrdinal

public static int atom1TypeOrdinal

atom2TypeOrdinal

public static int atom2TypeOrdinal

atomTypeOrdinal

public static int atomTypeOrdinal

summaAttribute

private static SummaAttribute summaAttribute

atomEnergies

public static double[] atomEnergies

Constructor Detail

AtomicPairwisePMFSumma

public AtomicPairwisePMFSumma(DistanceMatrix distanceMatrix,
                              double weight,
                              AtomicPairwisePMFSummaParameters parameters)

Method Detail

sumPerAtomType

public static final double[] sumPerAtomType()

sm2PerAtomType

public static final double[] sm2PerAtomType()

numberOfEachAtomType

public static int[] numberOfEachAtomType()

evaluate

public double evaluate()

Evaluates energy for each distance

Specified by:

evaluate in class AbstractEnergy

Returns:

a sum of all energy elements

evaluateAtoms

public void evaluateAtoms()

Describe evaluateAtoms method here.

Specified by:

evaluateAtoms in class AbstractEnergy

evaluate

public double evaluate(boolean evaluateAtoms)

evaluateElement

public double evaluateElement(Distance distance,
                              boolean evaluateAtoms)

test

public void test(TotalEnergy totalEnergy,
                 Atom atom)

Description copied from class: AbstractEnergy

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

Specified by:

test in class AbstractEnergy