meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain
Class CooperativeZRamachandran

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

All Implemented Interfaces:

CompositeTorsionsDefinitions, Attributable, Updateable

public class CooperativeZRamachandran
extends AbstractEnergy
implements CompositeTorsionsDefinitions

Created by IntelliJ IDEA. User: tetyanam Date: 09/06/2009 Time: 13:21:29 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 double[]	mean
private RamachandranSidechainEnergy	ramachandranSidechainEnergy
private ResidueTorsionsList	residueTorsionsList
private static double[]	std

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

CooperativeZRamachandran(RamachandranSidechainEnergy ramachandranSidechainEnergy, double weight, CooperativeZRamachandranParameters 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

mean

private static final double[] mean

std

private static final double[] std

ramachandranSidechainEnergy

private RamachandranSidechainEnergy ramachandranSidechainEnergy

residueTorsionsList

private ResidueTorsionsList residueTorsionsList

Constructor Detail

CooperativeZRamachandran

public CooperativeZRamachandran(RamachandranSidechainEnergy ramachandranSidechainEnergy,
                                double weight,
                                CooperativeZRamachandranParameters 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