Package ffx.openmm

Class CustomBondForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.CustomBondForce

Direct Known Subclasses:

BondForce, RestrainBondsForce

public class CustomBondForce
extends Force

Custom Bond Force.

Field Summary

Fields inherited from class ffx.openmm.Force

pointer

Constructor Summary

Constructors

Constructor	Description
CustomBondForce(String energy)	Custom Bond Force Constructor.

Method Summary

Modifier and Type	Method	Description
void	addBond(int i1, int i2, DoubleArray parameters)	Add a bond to the OpenMM System.
void	addGlobalParameter(String name, double value)	Add a global parameter to the CustomBondForce.
void	addPerBondParameter(String name)	Add a per-bond parameter to the CustomBondForce.
void	destroy()	Destroy the OpenMM CustomBondForce.
void	setBondParameters(int index, int i1, int i2, DoubleArray parameters)	Set the parameters for one bond in the OpenMM System.
void	updateParametersInContext(Context context)	Update the parameters in the OpenMM Context.

Methods inherited from class ffx.openmm.Force

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

Methods inherited from class java.lang.Object

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

Constructor Details

CustomBondForce

public CustomBondForce(String energy)

Custom Bond Force Constructor.

Parameters:

energy - The definition of the Energy.

Method Details

addBond

public void addBond(int i1,
 int i2,
 DoubleArray parameters)

Add a bond to the OpenMM System.

Parameters:

i1 - The index of the first atom.

i2 - The index of the second atom.

parameters - The bond parameters.

addPerBondParameter

public void addPerBondParameter(String name)

Add a per-bond parameter to the CustomBondForce.

Parameters:

name - The name of the parameter.

addGlobalParameter

public void addGlobalParameter(String name,
 double value)

Add a global parameter to the CustomBondForce.

Parameters:

name - The name of the parameter.

value - The value of the parameter.

setBondParameters

public void setBondParameters(int index,
 int i1,
 int i2,
 DoubleArray parameters)

Set the parameters for one bond in the OpenMM System.

Parameters:

index - The index of the bond.

i1 - The index of the first atom.

i2 - The index of the second atom.

parameters - The bond parameters.

updateParametersInContext

public void updateParametersInContext(Context context)

Update the parameters in the OpenMM Context.

Parameters:

context - The OpenMM Context.

destroy

public void destroy()

Destroy the OpenMM CustomBondForce.