AmoebaStretchBendForce Class Reference

This class implements the Amoeba stretch-bend interaction. More...

Inheritance diagram for AmoebaStretchBendForce:

List of all members.

Public Member Functions
def	getNumStretchBends
	getNumStretchBends(self) -> int
def	addStretchBend
	addStretchBend(self, particle1, particle2, particle3, lengthAB, lengthCB, angle, k1, k2) -> int
def	getStretchBendParameters
	Get the force field parameters for a stretch-bend term.
def	setStretchBendParameters
	Set the force field parameters for a stretch-bend term.
def	updateParametersInContext
	Update the per-stretch-bend term parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaStretchBendForce __init__(self, other) -> AmoebaStretchBendForce
Public Attributes
	this

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Detailed Description

This class implements the Amoeba stretch-bend interaction.

To use it, create a StretchBendForce object then call addStretchBend() once for each stretch-bend. After a stretch-bend has been added, you can modify its force field parameters by calling setStretchBendParameters(). 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) -> AmoebaStretchBendForce __init__(self, other) -> AmoebaStretchBendForce

Create an AmoebaStretchBendForce.

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Member Function Documentation

def addStretchBend	(		self,
			particle1,
			particle2,
			particle3,
			lengthAB,
			lengthCB,
			angle,
			k1,
			k2
	)

addStretchBend(self, particle1, particle2, particle3, lengthAB, lengthCB, angle, k1, k2) -> int

Add a stretch-bend term to the force field.

Parameters:

particle1	(int) the index of the first particle connected by the stretch-bend
particle2	(int) the index of the second particle connected by the stretch-bend
particle3	(int) the index of the third particle connected by the stretch-bend
lengthAB	(double) the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCB	(double) the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
angle	(double) the equilibrium angle in radians
k1	(double) the force constant of the product of bond ab and angle a-b-c
k2	(double) the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1)

Returns:

(int) the index of the stretch-bend that was added

def getNumStretchBends

(

self

)

getNumStretchBends(self) -> int

Get the number of stretch-bend terms in the potential function

def getStretchBendParameters	(		self,
			index
	)

Get the force field parameters for a stretch-bend term.

Parameters:

index

(int) the index of the stretch-bend for which to get parameters

Returns:

(int) the index of the first particle connected by the stretch-bend

(int) the index of the second particle connected by the stretch-bend

(int) the index of the third particle connected by the stretch-bend

(double) the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm

(double) the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm

(double) the equilibrium angle in radians

(double) the force constant of the product of bond ab and angle a-b-c

(double) the force constant of the product of bond bc and angle a-b-c

def setStretchBendParameters	(		self,
			index,
			particle1,
			particle2,
			particle3,
			lengthAB,
			lengthCB,
			angle,
			k1,
			k2
	)

Set the force field parameters for a stretch-bend term.

Parameters:

index	(int) the index of the stretch-bend for which to set parameters
particle1	(int) the index of the first particle connected by the stretch-bend
particle2	(int) the index of the second particle connected by the stretch-bend
particle3	(int) the index of the third particle connected by the stretch-bend
lengthAB	(double) the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCB	(double) the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
angle	(double) the equilibrium angle in radians
k1	(double) the force constant of the product of bond ab and angle a-b-c
k2	(double) the force constant of the product of bond bc and angle a-b-c (optional, default is the same as k1)

def updateParametersInContext	(		self,
			context
	)

Update the per-stretch-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 setStretchBendParameters() 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-stretch-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