Package ffx.openmm

Class HarmonicAngleForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.HarmonicAngleForce

public class HarmonicAngleForce
extends Force

This class implements an interaction between groups of three particles that varies harmonically with the angle between them. To use it, create a HarmonicAngleForce object then call addAngle() once for each angle. After an angle has been added, you can modify its force field parameters by calling setAngleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Field Summary

Fields inherited from class ffx.openmm.Force

pointer

Constructor Summary

Constructors

Constructor	Description
HarmonicAngleForce()	Create a new HarmonicAngleForce.

Method Summary

Modifier and Type	Method	Description
int	addAngle(int particle1, int particle2, int particle3, double angle, double k)	Add an angle term to the force field.
void	destroy()	Destroy the force.
void	getAngleParameters(int index, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.IntByReference particle3, com.sun.jna.ptr.DoubleByReference angle, com.sun.jna.ptr.DoubleByReference k)	Get the force field parameters for an angle term.
void	getAngleParameters(int index, IntBuffer particle1, IntBuffer particle2, IntBuffer particle3, DoubleBuffer angle, DoubleBuffer k)	Get the force field parameters for an angle term.
int	getNumAngles()	Get the number of angles in the force.
void	setAngleParameters(int index, int particle1, int particle2, int particle3, double angle, double k)	Set the force field parameters for an angle term.
void	setUsesPeriodicBoundaryConditions(boolean periodic)	Set whether this force should apply periodic boundary conditions when calculating displacements.
void	updateParametersInContext(Context context)	Update the parameters in the OpenMM Context.
boolean	usesPeriodicBoundaryConditions()	Check if the force uses periodic boundary conditions.

Methods inherited from class ffx.openmm.Force

getForceGroup, getForceIndex, getName, getPointer, setForceGroup, setForceIndex, setName

Methods inherited from class java.lang.Object

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

Constructor Details

HarmonicAngleForce

public HarmonicAngleForce()

Create a new HarmonicAngleForce.

Method Details

addAngle

public int addAngle(int particle1,
 int particle2,
 int particle3,
 double angle,
 double k)

Add an angle term to the force field.

Parameters:

particle1 - The index of the first particle forming the angle.

particle2 - The index of the second particle forming the angle.

particle3 - The index of the third particle forming the angle.

angle - The equilibrium angle, measured in radians.

k - The harmonic force constant for the angle, measured in kJ/mol/radianˆ2.

Returns:

The index of the angle that was added.

destroy

public void destroy()

Destroy the force.

Specified by:

destroy in class Force

getAngleParameters

public void getAngleParameters(int index,
 com.sun.jna.ptr.IntByReference particle1,
 com.sun.jna.ptr.IntByReference particle2,
 com.sun.jna.ptr.IntByReference particle3,
 com.sun.jna.ptr.DoubleByReference angle,
 com.sun.jna.ptr.DoubleByReference k)

Get the force field parameters for an angle term.

Parameters:

index - The index of the angle for which to get parameters.

particle1 - The index of the first particle forming the angle (output).

particle2 - The index of the second particle forming the angle (output).

particle3 - The index of the third particle forming the angle (output).

angle - The equilibrium angle, measured in radians (output).

k - The harmonic force constant for the angle, measured in kJ/mol/radianˆ2 (output).

getAngleParameters

public void getAngleParameters(int index,
 IntBuffer particle1,
 IntBuffer particle2,
 IntBuffer particle3,
 DoubleBuffer angle,
 DoubleBuffer k)

Get the force field parameters for an angle term.

Parameters:

index - The index of the angle for which to get parameters.

particle1 - The index of the first particle forming the angle (output).

particle2 - The index of the second particle forming the angle (output).

particle3 - The index of the third particle forming the angle (output).

angle - The equilibrium angle, measured in radians (output).

k - The harmonic force constant for the angle, measured in kJ/mol/radianˆ2 (output).

getNumAngles

public int getNumAngles()

Get the number of angles in the force.

Returns:

The number of angles.

setAngleParameters

public void setAngleParameters(int index,
 int particle1,
 int particle2,
 int particle3,
 double angle,
 double k)

Set the force field parameters for an angle term.

Parameters:

index - The index of the angle for which to set parameters.

particle1 - The index of the first particle forming the angle.

particle2 - The index of the second particle forming the angle.

particle3 - The index of the third particle forming the angle.

angle - The equilibrium angle, measured in radians.

k - The harmonic force constant for the angle, measured in kJ/mol/radianˆ2.

setUsesPeriodicBoundaryConditions

public void setUsesPeriodicBoundaryConditions(boolean periodic)

Set whether this force should apply periodic boundary conditions when calculating displacements.

Parameters:

periodic - If true, periodic boundary conditions will be applied.

updateParametersInContext

public void updateParametersInContext(Context context)

Update the parameters in the OpenMM Context.

Parameters:

context - The OpenMM Context.

usesPeriodicBoundaryConditions

public boolean usesPeriodicBoundaryConditions()

Check if the force uses periodic boundary conditions.

Overrides:

usesPeriodicBoundaryConditions in class Force

Returns:

True if the force uses periodic boundary conditions.