AmoebaAngleForce Class Reference

This class implements an interaction between triplets of particles that varies with the angle between them. More...

Inheritance diagram for AmoebaAngleForce:

List of all members.

Public Member Functions
def	getNumAngles
	getNumAngles(self) -> int
def	setAmoebaGlobalAngleCubic
	Set the global cubic term.
def	getAmoebaGlobalAngleCubic
	getAmoebaGlobalAngleCubic(self) -> double
def	setAmoebaGlobalAngleQuartic
	Set the global quartic term.
def	getAmoebaGlobalAngleQuartic
	getAmoebaGlobalAngleQuartic(self) -> double
def	setAmoebaGlobalAnglePentic
	Set the global pentic term.
def	getAmoebaGlobalAnglePentic
	getAmoebaGlobalAnglePentic(self) -> double
def	setAmoebaGlobalAngleSextic
	Set the global sextic term.
def	getAmoebaGlobalAngleSextic
	getAmoebaGlobalAngleSextic(self) -> double
def	addAngle
	addAngle(self, particle1, particle2, particle3, length, quadraticK) -> int
def	getAngleParameters
	Get the force field parameters for an angle term.
def	setAngleParameters
	Set the force field parameters for an angle term.
def	updateParametersInContext
	Update the per-angle parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaAngleForce __init__(self, other) -> AmoebaAngleForce
Public Attributes
	this

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Detailed Description

This class implements an interaction between triplets of particles that varies with the angle between them.

The interaction is defined by a 6th order polynomial. Only the quadratic term is set per-angle. The coefficients of the higher order terms each have a single value that is set globally.

To use it, create an AmoebaAngleForce 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().

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

__init__(self) -> AmoebaAngleForce __init__(self, other) -> AmoebaAngleForce

Create an AmoebaAngleForce.

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Member Function Documentation

def addAngle	(		self,
			particle1,
			particle2,
			particle3,
			length,
			quadraticK
	)

addAngle(self, particle1, particle2, particle3, length, quadraticK) -> int

Add an angle term to the force field.

Parameters:

particle1	(int) the index of the first particle connected by the angle
particle2	(int) the index of the second particle connected by the angle
particle3	(int) the index of the third particle connected by the angle
length	(double) the equilibrium angle, measured in degrees
quadraticK	(double) the quadratic force constant for the angle, measured in kJ/mol/radian^2

Returns:

(int) the index of the angle that was added

def getAmoebaGlobalAngleCubic

(

self

)

getAmoebaGlobalAngleCubic(self) -> double

Get the global cubic term

Returns:

(double) global cubicK term

def getAmoebaGlobalAnglePentic

(

self

)

getAmoebaGlobalAnglePentic(self) -> double

Get the global pentic term

Returns:

(double) global penticK term

def getAmoebaGlobalAngleQuartic

(

self

)

getAmoebaGlobalAngleQuartic(self) -> double

Get the global quartic term

Returns:

(double) global quartic term

def getAmoebaGlobalAngleSextic

(

self

)

getAmoebaGlobalAngleSextic(self) -> double

Get the global sextic term

Returns:

(double) global sextic term

def getAngleParameters	(		self,
			index
	)

Get the force field parameters for an angle term.

Parameters:

index

(int) the index of the angle for which to get parameters

Returns:

(int) the index of the first particle connected by the angle

(int) the index of the second particle connected by the angle

(int) the index of the third particle connected by the angle

(double) the equilibrium angle, measured in degrees

(double) the quadratic force constant for the angle, measured in kJ/mol/radian^2

def getNumAngles

(

self

)

getNumAngles(self) -> int

Get the number of angle stretch terms in the potential function

def setAmoebaGlobalAngleCubic	(		self,
			cubicK
	)

Set the global cubic term.

Parameters:

cubicK

(double) the cubic force constant for the angle

def setAmoebaGlobalAnglePentic	(		self,
			penticK
	)

Set the global pentic term.

Parameters:

penticK

(double) the pentic force constant for the angle

def setAmoebaGlobalAngleQuartic	(		self,
			quarticK
	)

Set the global quartic term.

Parameters:

quarticK

(double) the quartic force constant for the angle

def setAmoebaGlobalAngleSextic	(		self,
			sexticK
	)

Set the global sextic term.

Parameters:

sexticK

(double) the sextic force constant for the angle

def setAngleParameters	(		self,
			index,
			particle1,
			particle2,
			particle3,
			length,
			quadraticK
	)

Set the force field parameters for an angle term.

Parameters:

index	(int) the index of the angle for which to set parameters
particle1	(int) the index of the first particle connected by the angle
particle2	(int) the index of the second particle connected by the angle
particle3	(int) the index of the third particle connected by the angle
length	(double) the equilibrium angle, measured in degrees
quadraticK	(double) the quadratic force constant for the angle, measured in kJ/mol/radian^2

def updateParametersInContext	(		self,
			context
	)

Update the per-angle parameters in a Context to match those stored in this Force object.

This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-angle parameters. The set of particles involved in an angle cannot be changed, nor can new angles be added.

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:

(bool) true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

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Member Data Documentation

this

Reimplemented from Force.

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The documentation for this class was generated from the following file:

• openmm.py