Package ffx.openmm

Class PeriodicTorsionForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.PeriodicTorsionForce

Direct Known Subclasses:

ImproperTorsionForce, RestrainTorsionsForce, TorsionForce

public class PeriodicTorsionForce
extends Force

This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them. To use it, create a PeriodicTorsionForce object then call addTorsion() once for each torsion. After a torsion has been added, you can modify its force field parameters by calling setTorsionParameters(). 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
PeriodicTorsionForce()	Create a new PeriodicTorsionForce.

Method Summary

Modifier and Type	Method	Description
int	addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k)	Add a torsion to the PeriodicTorsionForce.
void	destroy()	Destroy the force.
int	getNumTorsions()	Get the number of torsions in the force.
void	getTorsionParameters(int index, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.IntByReference particle3, com.sun.jna.ptr.IntByReference particle4, com.sun.jna.ptr.IntByReference periodicity, com.sun.jna.ptr.DoubleByReference phase, com.sun.jna.ptr.DoubleByReference k)	Get the parameters for a torsion.
void	getTorsionParameters(int index, IntBuffer particle1, IntBuffer particle2, IntBuffer particle3, IntBuffer particle4, IntBuffer periodicity, DoubleBuffer phase, DoubleBuffer k)	Get the parameters for a torsion.
void	setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k)	Set the parameters for a torsion.
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

PeriodicTorsionForce

public PeriodicTorsionForce()

Create a new PeriodicTorsionForce.

Method Details

addTorsion

public int addTorsion(int particle1,
 int particle2,
 int particle3,
 int particle4,
 int periodicity,
 double phase,
 double k)

Add a torsion to the PeriodicTorsionForce.

Parameters:

particle1 - Index of the first atom.

particle2 - Index of the second atom.

particle3 - Index of the third atom.

particle4 - Index of the fourth atom.

periodicity - The periodicity of the torsion.

phase - The phase of the torsion.

k - The force constant for the torsion.

Returns:

The index of the torsion that was added.

destroy

public void destroy()

Destroy the force.

Specified by:

destroy in class Force

getNumTorsions

public int getNumTorsions()

Get the number of torsions in the force.

Returns:

The number of torsions.

getTorsionParameters

public void getTorsionParameters(int index,
 com.sun.jna.ptr.IntByReference particle1,
 com.sun.jna.ptr.IntByReference particle2,
 com.sun.jna.ptr.IntByReference particle3,
 com.sun.jna.ptr.IntByReference particle4,
 com.sun.jna.ptr.IntByReference periodicity,
 com.sun.jna.ptr.DoubleByReference phase,
 com.sun.jna.ptr.DoubleByReference k)

Get the parameters for a torsion.

Parameters:

index - The index of the torsion.

particle1 - The index of the first atom (output).

particle2 - The index of the second atom (output).

particle3 - The index of the third atom (output).

particle4 - The index of the fourth atom (output).

periodicity - The periodicity of the torsion (output).

phase - The phase of the torsion (output).

k - The force constant for the torsion (output).

getTorsionParameters

public void getTorsionParameters(int index,
 IntBuffer particle1,
 IntBuffer particle2,
 IntBuffer particle3,
 IntBuffer particle4,
 IntBuffer periodicity,
 DoubleBuffer phase,
 DoubleBuffer k)

Get the parameters for a torsion.

Parameters:

index - The index of the torsion.

particle1 - The index of the first atom (output).

particle2 - The index of the second atom (output).

particle3 - The index of the third atom (output).

particle4 - The index of the fourth atom (output).

periodicity - The periodicity of the torsion (output).

phase - The phase of the torsion (output).

k - The force constant for the torsion (output).

setTorsionParameters

public void setTorsionParameters(int index,
 int particle1,
 int particle2,
 int particle3,
 int particle4,
 int periodicity,
 double phase,
 double k)

Set the parameters for a torsion.

Parameters:

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

particle1 - The index of the first atom in the torsion.

particle2 - The index of the second atom in the torsion.

particle3 - The index of the third atom in the torsion.

particle4 - The index of the fourth atom in the torsion.

periodicity - The periodicity of the torsion.

phase - The phase of the torsion.

k - The force constant for the torsion.

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.