This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups of particles. More...

Inheritance diagram for CustomCentroidBondForce:

Public Member Functions
def	getNumGroupsPerBond
	getNumGroupsPerBond(self) -> int
def	getNumGroups
	getNumGroups(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	addGroup
	addGroup(self, particles, weights) -> int addGroup(self, particles) -> int
def	getGroupParameters
	Get the properties of a group.
def	setGroupParameters
	Set the properties of a group.
def	addBond
	addBond(self, groups, parameters) -> int addBond(self, groups) -> 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	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, numGroups, energy) -> CustomCentroidBondForce __init__(self, other) -> CustomCentroidBondForce
Public Attributes
	this

Detailed Description

This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups of particles.

This is useful for a variety of purposes, such as restraints to keep two molecules from moving too far apart.

When using this class, you define groups of particles, and the center of each group is calculated as a weighted average of the particle positions. By default, the particle masses are used as weights, so the center position is the center of mass. You can optionally specify different weights to use. You then add bonds just as with CustomCompoundBondForce, but instead of specifying the particles that make up a bond, you specify the groups.

When creating a CustomCentroidBondForce, you specify the number of groups involved in a bond, and an expression for the energy of each bond. It may depend on the center positions of individual groups, the distances between the centers of pairs of groups, the angles formed by sets of three groups, and the dihedral angles formed by sets of four groups.

We refer to the groups in a bond as g1, g2, g3, etc. For each bond, CustomCentroidBondForce 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 centers of the groups. For example, x1 is the x coordinate of the center of group g1, and y3 is the y coordinate of the center of group g3.
distance(g1, g2): the distance between the centers of groups g1 and g2 (where "g1" and "g2" may be replaced by the names of whichever groups you want to calculate the distance between).
angle(g1, g2, g3): the angle formed by the centers of the three specified groups.
dihedral(g1, g2, g3, g4): the dihedral angle formed by the centers of the four specified groups.

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

To use this class, create a CustomCentroidBondForce 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 addGroup() to define the particle groups. Each group is specified by the particles it contains, and the weights to use when computing the center position.

Then 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 CustomCentroidBondForce that implements a harmonic force between the centers of mass of two groups of particles.


 CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "0.5*k*distance(g1,g2)^2");
 force->addPerBondParameter("k");
 force->addGroup(particles1);
 force->addGroup(particles2);
 vector<int> bondGroups;
 bondGroups.push_back(0);
 bondGroups.push_back(1);
 vector<double> bondParameters;
 bondParameters.push_back(k);
 force->addBond(bondGroups, bondParameters);

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, numGroups, energy) -> CustomCentroidBondForce __init__(self, other) -> CustomCentroidBondForce

Create a CustomCentroidBondForce.

Parameters:

numGroups	(int) the number of groups 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, groups, parameters) -> int addBond(self, groups) -> int

Add a bond to the force

Parameters:

groups	(vector< int >) the indices of the groups 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 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 addGroup	(	self,
		args
	)

addGroup(self, particles, weights) -> int addGroup(self, particles) -> int

Add a particle group.

Parameters:

particles	(vector< int >) the indices of the particles to include in the group
weights	(vector< double >) the weight to use for each particle when computing the center position. If this is omitted, then particle masses will be used as weights.

Returns:: (int) the index of the group 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 groups 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 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 getGroupParameters	(	self,
		index
	)

Get the properties of a group.

Parameters:

index (int) the index of the group to get

Returns:: (vector< int >) the indices of the particles in the group; (vector< double >) the weight used for each particle when computing the center position. If no weights were specified, this vector will be empty indicating that particle masses should be used as weights.

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 getNumGroups ( self )

getNumGroups(self) -> int

Get the number of particle groups that have been defined.

def getNumGroupsPerBond ( self )

getNumGroupsPerBond(self) -> int

Get the number of groups 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
groups	(vector< int >) the indices of the groups 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 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 setGroupParameters	(	self,
		args
	)

Set the properties of a group.

Parameters:

index	(int) the index of the group to set
particles	(vector< int >) the indices of the particles in the group
weights	(vector< double >) the weight to use for each particle when computing the center position. If this is omitted, then particle masses will be used as weights.

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. Neither the definitions of groups nor the set of groups involved in a bond can 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