AmoebaOutOfPlaneBendForce Class Reference

This class implements the Amoeba out-of-plane bend interaction. More...

Inheritance diagram for AmoebaOutOfPlaneBendForce:

List of all members.

Public Member Functions
def	getNumOutOfPlaneBends
	getNumOutOfPlaneBends(self) -> int
def	setAmoebaGlobalOutOfPlaneBendCubic
	Set the global cubic term.
def	getAmoebaGlobalOutOfPlaneBendCubic
	getAmoebaGlobalOutOfPlaneBendCubic(self) -> double
def	setAmoebaGlobalOutOfPlaneBendQuartic
	Set the global cubic term.
def	getAmoebaGlobalOutOfPlaneBendQuartic
	getAmoebaGlobalOutOfPlaneBendQuartic(self) -> double
def	setAmoebaGlobalOutOfPlaneBendPentic
	Set the global pentic term.
def	getAmoebaGlobalOutOfPlaneBendPentic
	getAmoebaGlobalOutOfPlaneBendPentic(self) -> double
def	setAmoebaGlobalOutOfPlaneBendSextic
	Set the global sextic term.
def	getAmoebaGlobalOutOfPlaneBendSextic
	getAmoebaGlobalOutOfPlaneBendSextic(self) -> double
def	addOutOfPlaneBend
	addOutOfPlaneBend(self, particle1, particle2, particle3, particle4, k) -> int
def	getOutOfPlaneBendParameters
	Get the force field parameters for an out-of-plane bend term.
def	setOutOfPlaneBendParameters
	Set the force field parameters for an out-of-plane bend term.
def	updateParametersInContext
	Update the per-bend term parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaOutOfPlaneBendForce __init__(self, other) -> AmoebaOutOfPlaneBendForce
Public Attributes
	this

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Detailed Description

This class implements the Amoeba out-of-plane bend interaction.

To use it, create an OutOfPlaneBendForce object then call addOutOfPlaneBend() once for each outOfPlaneBend. After an out-of-plane bend has been added, you can modify its force field parameters by calling setOutOfPlaneBendParameters(). 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) -> AmoebaOutOfPlaneBendForce __init__(self, other) -> AmoebaOutOfPlaneBendForce

Create an AmoebaOutOfPlaneBendForce.

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Member Function Documentation

def addOutOfPlaneBend	(		self,
			particle1,
			particle2,
			particle3,
			particle4,
			k
	)

addOutOfPlaneBend(self, particle1, particle2, particle3, particle4, k) -> int

Add an out-of-plane bend term to the force field.

Parameters:

particle1	(int) the index of the first particle connected by the outOfPlaneBend
particle2	(int) the index of the second particle connected by the outOfPlaneBend
particle3	(int) the index of the third particle connected by the outOfPlaneBend
particle4	(int) the index of the fourth particle connected by the outOfPlaneBend
k	(double) the force constant for the out-of-plane bend

Returns:

(int) the index of the out-of-plane bend that was added

def getAmoebaGlobalOutOfPlaneBendCubic

(

self

)

getAmoebaGlobalOutOfPlaneBendCubic(self) -> double

Get the global cubic term

Returns:

(double) global cubicK term

def getAmoebaGlobalOutOfPlaneBendPentic

(

self

)

getAmoebaGlobalOutOfPlaneBendPentic(self) -> double

Get the global pentic term

Returns:

(double) global penticK term

def getAmoebaGlobalOutOfPlaneBendQuartic

(

self

)

getAmoebaGlobalOutOfPlaneBendQuartic(self) -> double

Get the global quartic term

Returns:

(double) global quartic term

def getAmoebaGlobalOutOfPlaneBendSextic

(

self

)

getAmoebaGlobalOutOfPlaneBendSextic(self) -> double

Get the global sextic term

Returns:

(double) global sexticK term

def getNumOutOfPlaneBends

(

self

)

getNumOutOfPlaneBends(self) -> int

Get the number of out-of-plane bend terms in the potential function

def getOutOfPlaneBendParameters	(		self,
			index
	)

Get the force field parameters for an out-of-plane bend term.

Parameters:

index

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

Returns:

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

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

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

(int) the index of the fourth particle connected by the outOfPlaneBend

(double) the force constant for the out-of-plane bend

def setAmoebaGlobalOutOfPlaneBendCubic	(		self,
			cubicK
	)

Set the global cubic term.

Parameters:

cubicK

(double) the cubic force constant for the angle

def setAmoebaGlobalOutOfPlaneBendPentic	(		self,
			penticK
	)

Set the global pentic term.

Parameters:

penticK

(double) the pentic force constant for the angle

def setAmoebaGlobalOutOfPlaneBendQuartic	(		self,
			quarticK
	)

Set the global cubic term.

Parameters:

quarticK

(double) the quartic force constant for the angle

def setAmoebaGlobalOutOfPlaneBendSextic	(		self,
			sexticK
	)

Set the global sextic term.

Parameters:

sexticK

(double) the sextic force constant for the angle

def setOutOfPlaneBendParameters	(		self,
			index,
			particle1,
			particle2,
			particle3,
			particle4,
			k
	)

Set the force field parameters for an out-of-plane bend term.

Parameters:

index	(int) the index of the outOfPlaneBend for which to set parameters
particle1	(int) the index of the first particle connected by the outOfPlaneBend
particle2	(int) the index of the second particle connected by the outOfPlaneBend
particle3	(int) the index of the third particle connected by the outOfPlaneBend
particle4	(int) the index of the fourth particle connected by the outOfPlaneBend
k	(double) the force constant for the out-of-plane bend

def updateParametersInContext	(		self,
			context
	)

Update the per-bend term 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 setOutOfPlaneBendParameters() 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-bend term parameters. The set of particles involved in a term cannot be changed, nor can new terms 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