This class implements interactions between sets of three particles that depend on the angle between them. More...

Inheritance diagram for CustomAngleForce:

Public Member Functions
def	getNumAngles
	getNumAngles(self) -> int
def	getNumPerAngleParameters
	getNumPerAngleParameters(self) -> int
def	getNumGlobalParameters
	getNumGlobalParameters(self) -> int
def	getEnergyFunction
	getEnergyFunction(self) -> std::string const &
def	setEnergyFunction
	Set the algebraic expression that gives the interaction energy for each angle.
def	addPerAngleParameter
	addPerAngleParameter(self, name) -> int
def	getPerAngleParameterName
	getPerAngleParameterName(self, index) -> std::string const &
def	setPerAngleParameterName
	Set the name of a per-angle parameter.
def	addGlobalParameter
	addGlobalParameter(self, name, defaultValue) -> int
def	getGlobalParameterName
	getGlobalParameterName(self, index) -> std::string const &
def	setGlobalParameterName
	Set the name of a global parameter.
def	getGlobalParameterDefaultValue
	getGlobalParameterDefaultValue(self, index) -> double
def	setGlobalParameterDefaultValue
	Set the default value of a global parameter.
def	addAngle
	addAngle(self, particle1, particle2, particle3, parameters) -> int addAngle(self, particle1, particle2, particle3) -> 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, energy) -> CustomAngleForce __init__(self, other) -> CustomAngleForce
Public Attributes
	this

Detailed Description

This class implements interactions between sets of three particles that depend on the angle between them.

Unlike HarmonicAngleForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-angle parameters.

To use this class, create a CustomAngleForce object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the angle formed by the particles, as well as on any parameters you choose. Then call addPerAngleParameter() to define per-angle parameters, and addGlobalParameter() to define global parameters. The values of per-angle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter(). Finally, call addAngle() once for each angle. After an angle has been added, you can modify its parameters by calling setAngleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomAngleForce that implements a harmonic potential:

CustomAngleForce* force = new CustomAngleForce("0.5*k*(theta-theta0)^2");

This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:


 force->addPerAngleParameter("k");
 force->addPerAngleParameter("theta0");

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. select(x,y,z) = z if x = 0, y otherwise.

Constructor & Destructor Documentation

def __init__	(	self,
		args
	)

__init__(self, energy) -> CustomAngleForce __init__(self, other) -> CustomAngleForce

Create a CustomAngleForce.

Parameters:

energy (string) an algebraic expression giving the interaction energy between three particles as a function of theta, the angle between them

Member Function Documentation

def addAngle	(	self,
		args
	)

addAngle(self, particle1, particle2, particle3, parameters) -> int addAngle(self, particle1, particle2, particle3) -> 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
parameters	(vector< double >) the list of parameters for the new angle

Returns:: (int) the index of the angle that was added

def addGlobalParameter	(	self,
		name,
		defaultValue
	)

addGlobalParameter(self, name, defaultValue) -> int

Add a new global parameter that the interaction may depend on.

Parameters:

name	(string) the name of the parameter
defaultValue	(double) the default value of the parameter

Returns:: (int) the index of the parameter that was added

def addPerAngleParameter	(	self,
		name
	)

addPerAngleParameter(self, name) -> int

Add a new per-angle parameter that the interaction may depend on.

Parameters:

name	(string) the name of the parameter

Returns:: (int) the index of the parameter that was added

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; (vector< double >) the list of parameters for the angle

def getEnergyFunction ( self )

getEnergyFunction(self) -> std::string const &

Get the algebraic expression that gives the interaction energy for each angle

def getGlobalParameterDefaultValue	(	self,
		index
	)

getGlobalParameterDefaultValue(self, index) -> double

Get the default value of a global parameter.

Parameters:

index (int) the index of the parameter for which to get the default value

Returns:: (double) the parameter default value

def getGlobalParameterName	(	self,
		index
	)

getGlobalParameterName(self, index) -> std::string const &

Get the name of a global parameter.

Parameters:

index (int) the index of the parameter for which to get the name

Returns:: (string) the parameter name

def getNumAngles ( self )

getNumAngles(self) -> int

Get the number of angles for which force field parameters have been defined.

def getNumGlobalParameters ( self )

getNumGlobalParameters(self) -> int

Get the number of global parameters that the interaction depends on.

def getNumPerAngleParameters ( self )

getNumPerAngleParameters(self) -> int

Get the number of per-angle parameters that the interaction depends on.

def getPerAngleParameterName	(	self,
		index
	)

getPerAngleParameterName(self, index) -> std::string const &

Get the name of a per-angle parameter.

Parameters:

index (int) the index of the parameter for which to get the name

Returns:: (string) the parameter name

def setAngleParameters	(	self,
		args
	)

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
parameters	(vector< double >) the list of parameters for the angle

def setEnergyFunction	(	self,
		energy
	)

Set the algebraic expression that gives the interaction energy for each angle.

def setGlobalParameterDefaultValue	(	self,
		index,
		defaultValue
	)

Set the default value of a global parameter.

Parameters:

index	(int) the index of the parameter for which to set the default value
defaultValue	(double) the default value of the parameter

def setGlobalParameterName	(	self,
		index,
		name
	)

Set the name of a global parameter.

Parameters:

index	(int) the index of the parameter for which to set the name
name	(string) the name of the parameter

def setPerAngleParameterName	(	self,
		index,
		name
	)

Set the name of a per-angle parameter.

Parameters:

index	(int) the index of the parameter for which to set the name
name	(string) the name of the parameter

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.

This method has several limitations. The only information it updates is the values of per-angle parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a 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) false

Reimplemented from Force.

Member Data Documentation

this

Reimplemented from Force.

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

openmm.py

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation