Package ffx.openmm

Class RBTorsionForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.RBTorsionForce

public class RBTorsionForce
extends Force

This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential. To use it, create an RBTorsionForce 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
RBTorsionForce()	Create a new RBTorsionForce.

Method Summary

Modifier and Type	Method	Description
int	addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5)	Add a torsion to the force.
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.DoubleByReference c0, com.sun.jna.ptr.DoubleByReference c1, com.sun.jna.ptr.DoubleByReference c2, com.sun.jna.ptr.DoubleByReference c3, com.sun.jna.ptr.DoubleByReference c4, com.sun.jna.ptr.DoubleByReference c5)	Get the parameters for a torsion.
void	getTorsionParameters(int index, IntBuffer particle1, IntBuffer particle2, IntBuffer particle3, IntBuffer particle4, DoubleBuffer c0, DoubleBuffer c1, DoubleBuffer c2, DoubleBuffer c3, DoubleBuffer c4, DoubleBuffer c5)	Get the parameters for a torsion.
void	setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5)	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

RBTorsionForce

public RBTorsionForce()

Create a new RBTorsionForce.

Method Details

addTorsion

public int addTorsion(int particle1,
 int particle2,
 int particle3,
 int particle4,
 double c0,
 double c1,
 double c2,
 double c3,
 double c4,
 double c5)

Add a torsion to the force.

Parameters:

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

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

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

particle4 - The index of the fourth particle forming the torsion.

c0 - The C0 RB parameter.

c1 - The C1 RB parameter.

c2 - The C2 RB parameter.

c3 - The C3 RB parameter.

c4 - The C4 RB parameter.

c5 - The C5 RB parameter.

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.DoubleByReference c0,
 com.sun.jna.ptr.DoubleByReference c1,
 com.sun.jna.ptr.DoubleByReference c2,
 com.sun.jna.ptr.DoubleByReference c3,
 com.sun.jna.ptr.DoubleByReference c4,
 com.sun.jna.ptr.DoubleByReference c5)

Get the parameters for a torsion.

Parameters:

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

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

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

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

particle4 - The index of the fourth particle forming the torsion (output).

c0 - The C0 RB parameter (output).

c1 - The C1 RB parameter (output).

c2 - The C2 RB parameter (output).

c3 - The C3 RB parameter (output).

c4 - The C4 RB parameter (output).

c5 - The C5 RB parameter (output).

getTorsionParameters

public void getTorsionParameters(int index,
 IntBuffer particle1,
 IntBuffer particle2,
 IntBuffer particle3,
 IntBuffer particle4,
 DoubleBuffer c0,
 DoubleBuffer c1,
 DoubleBuffer c2,
 DoubleBuffer c3,
 DoubleBuffer c4,
 DoubleBuffer c5)

Get the parameters for a torsion.

Parameters:

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

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

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

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

particle4 - The index of the fourth particle forming the torsion (output).

c0 - The C0 RB parameter (output).

c1 - The C1 RB parameter (output).

c2 - The C2 RB parameter (output).

c3 - The C3 RB parameter (output).

c4 - The C4 RB parameter (output).

c5 - The C5 RB parameter (output).

setTorsionParameters

public void setTorsionParameters(int index,
 int particle1,
 int particle2,
 int particle3,
 int particle4,
 double c0,
 double c1,
 double c2,
 double c3,
 double c4,
 double c5)

Set the parameters for a torsion.

Parameters:

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

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

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

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

particle4 - The index of the fourth particle forming the torsion.

c0 - The C0 RB parameter.

c1 - The C1 RB parameter.

c2 - The C2 RB parameter.

c3 - The C3 RB parameter.

c4 - The C4 RB parameter.

c5 - The C5 RB parameter.

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.