meshi.energy.simpleEnergyTerms.alphaTorsion
Class AlphaTorsionEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement

All Implemented Interfaces:

MeshiPotential

public class AlphaTorsionEnergyElement
extends EnergyElement
implements MeshiPotential

Field Summary

private Atom	atom1
private Atom	atom2
private Atom	atom3
private Atom	atom4
private double	BUFF
private double	cyclicMidTor
private double	hiTor
private double	INV_BUFF
private double	loTor
private double	midTor
private boolean	on
private Torsion	torsion
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

AlphaTorsionEnergyElement(Torsion torsion, AlphaTorsionParameters param, double weight)
An energy element handling one alpha torsion.

Method Summary

Atom	atom1()
Atom	atom2()
Atom	atom3()
Atom	atom4()
private int	calc(double tor, double loTor, double hiTor, double[] ans)
double	evaluate()
Torsion	getTorsion()
boolean	isOn()
protected void	setAtoms()
java.lang.String	toString()
void	turnOff()
void	turnOn()
double	weight()

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

atom4

private Atom atom4

torsion

private Torsion torsion

loTor

private double loTor

hiTor

private double hiTor

midTor

private double midTor

cyclicMidTor

private double cyclicMidTor

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

on

private boolean on

Constructor Detail

AlphaTorsionEnergyElement

public AlphaTorsionEnergyElement(Torsion torsion,
                                 AlphaTorsionParameters param,
                                 double weight)

An energy element handling one alpha torsion. It checks for the secondary structure the torsion is in, and then assign the proper CA torsion range.

Method Detail

calc

private int calc(double tor,
                 double loTor,
                 double hiTor,
                 double[] ans)

weight

public double weight()

evaluate

public double evaluate()

Specified by:

evaluate in class EnergyElement

getTorsion

public Torsion getTorsion()

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()

atom4

public Atom atom4()

isOn

public boolean isOn()

turnOn

public void turnOn()

turnOff

public void turnOff()