meshi.energy.simpleEnergyTerms.alphaAngle
Class AlphaAngleEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement

All Implemented Interfaces:

MeshiPotential

public class AlphaAngleEnergyElement
extends EnergyElement
implements MeshiPotential

Field Summary

private Angle	angle
private Atom	atom1
private Atom	atom2
private Atom	atom3
private double	BUFF
double	force
double	force2
private double	hiAng
private double	infForce
private double	infForce3
private double	INV_BUFF
private double	loAng
private boolean	on
private double	weight

Fields inherited from class meshi.energy.EnergyElement

atoms, dFormatSrt, dFormatStd, DX, frozen, relativeDiffTolerance, VERY_SMALL, XYZ

Fields inherited from interface meshi.parameters.MeshiPotential

ACCESSIBLE, ALPHA_ANGLE_PARAMETERS, ALPHA_TORSION_PARAMETERS, ANGLE_PARAMETERS, ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, BOND_PARAMETERS, BURIED, COIL, COMPOSITE_PROPENSITY_2D_PARAMETERS, COMPOSITE_PROPENSITY_2D_WITH_PP_PARAMETERS, COMPOSITE_PROPENSITY_PARAMETERS, COMPOSITE_TORSIONS_PARAMETERS, CONTACTS_ENVIRONMENT_PARAMETERS, CONTACTS_PARAMETERS, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, COOPERATIVE_PROPENSITY_PARAMETERS, COOPERATIVE_RAMACHANDRAN_PARAMETERS, ELECTROSTATICS_PARAMETERS, EXCLUDED_VOL_PARAMETERS, FLAT_RAMACH_PARAMETERS, HELIX, HELIX_OR_COIL, HYDROGEN_BONDS_PAIRS_BETA_PARAMETERS, HYDROGEN_BONDS_PAIRS_HELIX_PARAMETERS, HYDROGEN_BONDS_PAIRS_PARAMETERS_SURFACE, LENNARD_JONES_PARAMETERS, LENNARD_JONES_PARAMETERS_BACKBONE, LENNARD_JONES_PARAMETERS_CA, LJ_ENVIRONMENT_PARAMETERS, LJ_ENVIRONMENT_PARAMETERS_BACKBONE, LJ_ENVIRONMENT_PARAMETERS_CA, ONE_ANGLE_PARAMETERS, OUT_OF_PLANE_PARAMETERS, PLANE_PARAMETERS, PROPENSITY_ANGLE_PARAMETERS, PROPENSITY_TORSION_PARAMETERS, SHEET, SHEET_OR_COIL, SOLVATE_LONG_HB_PARAMETERS, SOLVATE_MINIMIZE_HB_PARAMETERS, SOLVATE_NOHB_PARAMETERS, SOLVATE_PARAMETERS, SOLVATE_SC_PARAMETERS, TWO_ANGLES_PARAMETERS, TWO_TORSIONS_PARAMETERS

Constructor Summary

AlphaAngleEnergyElement(Angle angle, AlphaAngleParameters param, double weight)
The constructor needs a CA3 angle.

Method Summary

Atom	atom1()
Atom	atom2()
Atom	atom3()
double	evaluate() Angle energy calculation and atom forces updating.
Angle	getAngle()
boolean	isOn()
protected void	setAtoms()
java.lang.String	toString()
void	turnOff()
void	turnOn()

Methods inherited from class meshi.energy.EnergyElement

atoms, evaluateAtoms, frozen, test, updateFrozen

Methods inherited from class java.lang.Object

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

Field Detail

atom1

private Atom atom1

atom2

private Atom atom2

atom3

private Atom atom3

angle

private Angle angle

loAng

private double loAng

hiAng

private double hiAng

weight

private double weight

BUFF

private final double BUFF

See Also:

Constant Field Values

INV_BUFF

private final double INV_BUFF

See Also:

Constant Field Values

infForce

private final double infForce

See Also:

Constant Field Values

infForce3

private final double infForce3

See Also:

Constant Field Values

force

public double force

force2

public double force2

on

private boolean on

Constructor Detail

AlphaAngleEnergyElement

public AlphaAngleEnergyElement(Angle angle,
                               AlphaAngleParameters param,
                               double weight)

The constructor needs a CA3 angle. It checks for the secondary structure the angle is in, and then assign the proper CA3 angle range.

Method Detail

evaluate

public double evaluate()

Angle energy calculation and atom forces updating.

Specified by:

evaluate in class EnergyElement

getAngle

public Angle getAngle()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setAtoms

protected void setAtoms()

Specified by:

setAtoms in class EnergyElement

atom1

public Atom atom1()

atom2

public Atom atom2()

atom3

public Atom atom3()

isOn

public boolean isOn()

turnOn

public void turnOn()

turnOff

public void turnOff()