This class supports a wide variety of bonded interactions. More...

Inheritance diagram for CustomCompoundBondForce:

Public Member Functions
def	getNumParticlesPerBond
	getNumParticlesPerBond(self) -> int
def	getNumBonds
	getNumBonds(self) -> int
def	getNumPerBondParameters
	getNumPerBondParameters(self) -> int
def	getNumGlobalParameters
	getNumGlobalParameters(self) -> int
def	getNumTabulatedFunctions
	getNumTabulatedFunctions(self) -> int
def	getNumFunctions
	getNumFunctions(self) -> int
def	getEnergyFunction
	getEnergyFunction(self) -> std::string const &
def	setEnergyFunction
	Set the algebraic expression that gives the interaction energy of each bond.
def	addPerBondParameter
	addPerBondParameter(self, name) -> int
def	getPerBondParameterName
	getPerBondParameterName(self, index) -> std::string const &
def	setPerBondParameterName
	Set the name of a per-bond 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	addBond
	addBond(self, particles, parameters) -> int addBond(self, particles) -> int
def	getBondParameters
	Get the properties of a bond.
def	setBondParameters
	Set the properties of a bond.
def	addTabulatedFunction
	addTabulatedFunction(self, name, function) -> int
def	getTabulatedFunction
	getTabulatedFunction(self, index) -> TabulatedFunction getTabulatedFunction(self, index) -> TabulatedFunction
def	getTabulatedFunctionName
	getTabulatedFunctionName(self, index) -> std::string const &
def	addFunction
	addFunction(self, name, values, min, max) -> int
def	getFunctionParameters
	Get the parameters for a tabulated function that may appear in the energy expression.
def	setFunctionParameters
	Set the parameters for a tabulated function that may appear in the energy expression.
def	updateParametersInContext
	Update the per-bond parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self, numParticles, energy) -> CustomCompoundBondForce __init__(self, other) -> CustomCompoundBondForce
Public Attributes
	this

Detailed Description

This class supports a wide variety of bonded interactions.

It defines a "bond" as a single energy term that depends on the positions of a fixed set of particles. The number of particles involved in a bond, and how the energy depends on their positions, is configurable. It may depend on the positions of individual particles, the distances between pairs of particles, the angles formed by sets of three particles, and the dihedral angles formed by sets of four particles.

We refer to the particles in a bond as p1, p2, p3, etc. For each bond, CustomCompoundBondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on the following variables and functions:

x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the particle positions. For example, x1 is the x coordinate of particle p1, and y3 is the y coordinate of particle p3.
distance(p1, p2): the distance between particles p1 and p2 (where "p1" and "p2" may be replaced by the names of whichever particles you want to calculate the distance between).
angle(p1, p2, p3): the angle formed by the three specified particles.
dihedral(p1, p2, p3, p4): the dihedral angle formed by the four specified particles.

The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.

To use this class, create a CustomCompoundBondForce object, passing an algebraic expression to the constructor that defines the interaction energy of each bond. Then call addPerBondParameter() to define per-bond parameters and addGlobalParameter() to define global parameters. The values of per-bond parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().

Next, call addBond() to define bonds and specify their parameter values. After a bond has been added, you can modify its parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomCompoundBondForce that implements a Urey-Bradley potential. This is an interaction between three particles that depends on the angle formed by p1-p2-p3, and on the distance between p1 and p3.

CustomCompoundBondForce* force = new CustomCompoundBondForce(3, "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");

This force depends on four parameters: kangle, kbond, theta0, and r0. The following code defines these as per-bond parameters:


 force->addPerBondParameter("kangle");
 force->addPerBondParameter("kbond");
 force->addPerBondParameter("theta0");
 force->addPerBondParameter("r0");

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.

In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by creating a TabulatedFunction object. That function can then appear in the expression.

Constructor & Destructor Documentation

def __init__	(	self,
		args
	)

__init__(self, numParticles, energy) -> CustomCompoundBondForce __init__(self, other) -> CustomCompoundBondForce

Create a CustomCompoundBondForce.

Parameters:

numParticles	(int) the number of particles used to define each bond
energy	(string) an algebraic expression giving the interaction energy of each bond as a function of particle positions, inter-particle distances, angles, and dihedrals, and any global and per-bond parameters

Member Function Documentation

def addBond	(	self,
		args
	)

addBond(self, particles, parameters) -> int addBond(self, particles) -> int

Add a bond to the force

Parameters:

particles	(vector< int >) the indices of the particles the bond depends on
parameters	(vector< double >) the list of per-bond parameter values for the new bond

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

def addFunction	(	self,
		name,
		values,
		min,
		max
	)

addFunction(self, name, values, min, max) -> int

Add a tabulated function that may appear in the energy expression.

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 addPerBondParameter	(	self,
		name
	)

addPerBondParameter(self, name) -> int

Add a new per-bond 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 addTabulatedFunction	(	self,
		name,
		function
	)

addTabulatedFunction(self, name, function) -> int

Add a tabulated function that may appear in the energy expression.

Parameters:

name	(string) the name of the function as it appears in expressions
function	(TabulatedFunction *) a TabulatedFunction object defining the function. The TabulatedFunction should have been created on the heap with the "new" operator. The Force takes over ownership of it, and deletes it when the Force itself is deleted.

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

def getBondParameters	(	self,
		index
	)

Get the properties of a bond.

Parameters:

index (int) the index of the bond to get

Returns:: (vector< int >) the indices of the particles in the bond; (vector< double >) the list of per-bond parameter values for the bond

def getEnergyFunction ( self )

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

Get the algebraic expression that gives the interaction energy of each bond

def getFunctionParameters	(	self,
		index
	)

Get the parameters for a tabulated function that may appear in the energy expression.

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 getNumBonds ( self )

getNumBonds(self) -> int

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

def getNumFunctions ( self )

getNumFunctions(self) -> int

Get the number of tabulated functions that have been defined.

def getNumGlobalParameters ( self )

getNumGlobalParameters(self) -> int

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

def getNumParticlesPerBond ( self )

getNumParticlesPerBond(self) -> int

Get the number of particles used to define each bond.

def getNumPerBondParameters ( self )

getNumPerBondParameters(self) -> int

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

def getNumTabulatedFunctions ( self )

getNumTabulatedFunctions(self) -> int

Get the number of tabulated functions that have been defined.

def getPerBondParameterName	(	self,
		index
	)

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

Get the name of a per-bond parameter.

Parameters:

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

Returns:: (string) the parameter name

def getTabulatedFunction	(	self,
		args
	)

getTabulatedFunction(self, index) -> TabulatedFunction getTabulatedFunction(self, index) -> TabulatedFunction

Get a reference to a tabulated function that may appear in the energy expression.

Parameters:

index (int) the index of the function to get

Returns:: (TabulatedFunction) the TabulatedFunction object defining the function

def getTabulatedFunctionName	(	self,
		index
	)

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

Get the name of a tabulated function that may appear in the energy expression.

Parameters:

index (int) the index of the function to get

Returns:: (string) the name of the function as it appears in expressions

def setBondParameters	(	self,
		args
	)

Set the properties of a bond.

Parameters:

index	(int) the index of the bond to set
particles	(vector< int >) the indices of the particles in the bond
parameters	(vector< double >) the list of per-bond parameter values for the bond

def setEnergyFunction	(	self,
		energy
	)

Set the algebraic expression that gives the interaction energy of each bond.

def setFunctionParameters	(	self,
		index,
		name,
		values,
		min,
		max
	)

Set the parameters for a tabulated function that may appear in the energy expression.

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 setPerBondParameterName	(	self,
		index,
		name
	)

Set the name of a per-bond 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-bond 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 setBondParameters() 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-bond 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 bond cannot be changed, nor can new bonds 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