meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Class CooperativeRamachandran

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran

All Implemented Interfaces:

CompositeTorsionsDefinitions, Attributable, Updateable

public class CooperativeRamachandran
extends AbstractEnergy
implements CompositeTorsionsDefinitions

Nested Class Summary

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

AbstractEnergy.UpdateableList

Field Summary

private static double	diff
private double[]	diffSigma
private static double	factor
private static int	n
static int	numberOfResidueTypes
private RamachandranSidechainEnergy	ramachandranSidechainEnergy
private static Residue	residue
private ResidueTorsionsList	residueTorsionsList
private double[]	sumPerResidueType
private double[]	targetSigma
private static ResidueType	type

Fields inherited from class meshi.energy.AbstractEnergy

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

Fields inherited from interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions

ALL, CHI_1, CHI_2, CHI_3, CHI_4, COIL, HELIX, NUM_SIDECHAIN_TORSIONS, OMG, OMNI, PHI, POLYNOMIAL_CHI_1, POLYNOMIAL_CHI_1_CHI_2, POLYNOMIAL_CHI_1_CHI_2_TORSIONS, POLYNOMIAL_CHI_1_CHI_3, POLYNOMIAL_CHI_1_CHI_3_TORSIONS, POLYNOMIAL_CHI_1_CHI_4, POLYNOMIAL_CHI_1_CHI_4_TORSIONS, POLYNOMIAL_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI, POLYNOMIAL_PHI_PSI_CHI_1, POLYNOMIAL_PHI_PSI_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI_TORSIONS, PREPRO, PSI, SHEET, TOTAL_TORSION_ANGLES, UNIDENTIFIED_TORSION_TYPE

Constructor Summary

CooperativeRamachandran(RamachandranSidechainEnergy ramachandranSidechainEnergy, double weight, CooperativeRamachandranParameters parameters)

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 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

targetSigma

private final double[] targetSigma

diffSigma

private final double[] diffSigma

sumPerResidueType

private double[] sumPerResidueType

numberOfResidueTypes

public static final int numberOfResidueTypes

residue

private static Residue residue

type

private static ResidueType type

diff

private static double diff

factor

private static double factor

n

private static int n

ramachandranSidechainEnergy

private RamachandranSidechainEnergy ramachandranSidechainEnergy

residueTorsionsList

private ResidueTorsionsList residueTorsionsList

Constructor Detail

CooperativeRamachandran

public CooperativeRamachandran(RamachandranSidechainEnergy ramachandranSidechainEnergy,
                               double weight,
                               CooperativeRamachandranParameters parameters)

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)

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