CustomHbondForce Class Reference

This class supports a wide variety of energy functions used to represent hydrogen bonding. More...

Inheritance diagram for CustomHbondForce:

List of all members.

Public Member Functions
def	getNumDonors
	getNumDonors(self) -> int
def	getNumAcceptors
	getNumAcceptors(self) -> int
def	getNumExclusions
	getNumExclusions(self) -> int
def	getNumPerDonorParameters
	getNumPerDonorParameters(self) -> int
def	getNumPerAcceptorParameters
	getNumPerAcceptorParameters(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 between a donor and an acceptor.
def	getNonbondedMethod
	getNonbondedMethod(self) -> OpenMM::CustomHbondForce::NonbondedMethod
def	setNonbondedMethod
	Set the method used for handling long range nonbonded interactions.
def	getCutoffDistance
	getCutoffDistance(self) -> double
def	setCutoffDistance
	Set the cutoff distance (in nm) being used.
def	addPerDonorParameter
	addPerDonorParameter(self, name) -> int
def	getPerDonorParameterName
	getPerDonorParameterName(self, index) -> std::string const &
def	setPerDonorParameterName
	Set the name of a per-donor parameter.
def	addPerAcceptorParameter
	addPerAcceptorParameter(self, name) -> int
def	getPerAcceptorParameterName
	getPerAcceptorParameterName(self, index) -> std::string const &
def	setPerAcceptorParameterName
	Set the name of a per-acceptor 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	addDonor
	addDonor(self, d1, d2, d3, parameters) -> int addDonor(self, d1, d2, d3) -> int
def	getDonorParameters
	Get the properties of a donor group.
def	setDonorParameters
	Set the properties of a donor group.
def	addAcceptor
	addAcceptor(self, a1, a2, a3, parameters) -> int addAcceptor(self, a1, a2, a3) -> int
def	getAcceptorParameters
	Get the properties of an acceptor group.
def	setAcceptorParameters
	Set the properties of an acceptor group.
def	addExclusion
	addExclusion(self, donor, acceptor) -> int
def	getExclusionParticles
	Get the donor and acceptor in a pair whose interaction should be excluded.
def	setExclusionParticles
	Get the donor and acceptor in a pair whose interaction should be excluded.
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-donor and per-acceptor parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self, energy) -> CustomHbondForce __init__(self, other) -> CustomHbondForce
Public Attributes
	this
Static Public Attributes
	NoCutoff = _openmm.CustomHbondForce_NoCutoff
	CutoffNonPeriodic = _openmm.CustomHbondForce_CutoffNonPeriodic
	CutoffPeriodic = _openmm.CustomHbondForce_CutoffPeriodic

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Detailed Description

This class supports a wide variety of energy functions used to represent hydrogen bonding.

It computes interactions between "donor" particle groups and "acceptor" particle groups, where each group may include up to three particles. Typically a donor group consists of a hydrogen atom and the atoms it is bonded to, and an acceptor group consists of a negatively charged atom and the atoms it is bonded to.

We refer to the particles in a donor group as d1, d2 and d3, and the particles in an acceptor group as a1, a2, and a3. For each donor and each acceptor, CustomHbondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on arbitrary distances, angles, and dihedral angles defined by any of the six particles involved. The function distance(p1, p2) is the distance between the particles p1 and p2 (where "p1" and "p2" should be replaced by the names of the actual particles to calculate the distance between), angle(p1, p2, p3) is the angle formed by the three specified particles, and dihedral(p1, p2, p3, p4) is the dihedral angle formed by the four specified particles.

The expression also may involve tabulated functions, and may depend on arbitrary global, per-donor, and per-acceptor parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.

To use this class, create a CustomHbondForce object, passing an algebraic expression to the constructor that defines the interaction energy between each donor and acceptor. Then call addPerDonorParameter() to define per-donor parameters, addPerAcceptorParameter() to define per-acceptor parameters, and addGlobalParameter() to define global parameters. The values of per-donor and per-acceptor 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 addDonor() and addAcceptor() to define donors and acceptors and specify their parameter values. After a donor or acceptor has been added, you can modify its parameters by calling setDonorParameters() or setAcceptorParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

CustomHbondForce also lets you specify "exclusions", particular combinations of donors and acceptors whose interactions should be omitted from force and energy calculations. This is most often used for particles that are bonded to each other.

As an example, the following code creates a CustomHbondForce that implements a simple harmonic potential to keep the distance between a1 and d1, and the angle formed by a1-d1-d2, near ideal values:

CustomHbondForce* force = new CustomHbondForce("k*(distance(a1,d1)-r0)^2*(angle(a1,d1,d2)-theta0)^2");

This force depends on three parameters: k, r0, and theta0. The following code defines these as per-donor parameters:

 force->addPerDonorParameter("k");
 force->addPerDonorParameter("r0");
 force->addPerDonorParameter("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.

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.

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

Create a CustomHbondForce.

Parameters:

energy

(string) an algebraic expression giving the interaction energy between a donor and an acceptor as a function of inter-particle distances, angles, and dihedrals, as well as any global, per-donor, and per-acceptor parameters

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Member Function Documentation

def addAcceptor	(		self,
			args
	)

addAcceptor(self, a1, a2, a3, parameters) -> int addAcceptor(self, a1, a2, a3) -> int

Add an acceptor group to the force

Parameters:

a1	(int) the index of the first particle for this acceptor group
a2	(int) the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
a3	(int) the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
parameters	(vector< double >) the list of per-acceptor parameter values for the new acceptor

Returns:

(int) the index of the acceptor that was added

def addDonor	(		self,
			args
	)

addDonor(self, d1, d2, d3, parameters) -> int addDonor(self, d1, d2, d3) -> int

Add a donor group to the force

Parameters:

d1	(int) the index of the first particle for this donor group
d2	(int) the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
d3	(int) the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
parameters	(vector< double >) the list of per-donor parameter values for the new donor

Returns:

(int) the index of the donor that was added

def addExclusion	(		self,
			donor,
			acceptor
	)

addExclusion(self, donor, acceptor) -> int

Add a donor-acceptor pair to the list of interactions that should be excluded.

Parameters:

donor	(int) the index of the donor to exclude
acceptor	(int) the index of the acceptor to exclude

Returns:

(int) the index of the exclusion 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 addPerAcceptorParameter	(		self,
			name
	)

addPerAcceptorParameter(self, name) -> int

Add a new per-acceptor 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 addPerDonorParameter	(		self,
			name
	)

addPerDonorParameter(self, name) -> int

Add a new per-donor 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 getAcceptorParameters	(		self,
			index
	)

Get the properties of an acceptor group.

Parameters:

index

(int) the index of the acceptor group to get

Returns:

(int) the index of the first particle for this acceptor group

(int) the index of the second particle for this acceptor group. If the group only includes one particle, this will be -1.

(int) the index of the third particle for this acceptor group. If the group includes less than three particles, this will be -1.

(vector< double >) the list of per-acceptor parameter values for the acceptor

def getCutoffDistance

(

self

)

getCutoffDistance(self) -> double

Get the cutoff distance (in nm) being used. All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Returns:

(double) the cutoff distance, measured in nm

def getDonorParameters	(		self,
			index
	)

Get the properties of a donor group.

Parameters:

index

(int) the index of the donor group to get

Returns:

(int) the index of the first particle for this donor group

(int) the index of the second particle for this donor group. If the group only includes one particle, this will be -1.

(int) the index of the third particle for this donor group. If the group includes less than three particles, this will be -1.

(vector< double >) the list of per-donor parameter values for the donor

def getEnergyFunction

(

self

)

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

Get the algebraic expression that gives the interaction energy between a donor and an acceptor

def getExclusionParticles	(		self,
			index
	)

Get the donor and acceptor in a pair whose interaction should be excluded.

Parameters:

index

(int) the index of the exclusion for which to get donor and acceptor indices

Returns:

(int) the index of the donor

(int) the index of the acceptor

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 getNonbondedMethod

(

self

)

getNonbondedMethod(self) -> OpenMM::CustomHbondForce::NonbondedMethod

Get the method used for handling long range nonbonded interactions.

def getNumAcceptors

(

self

)

getNumAcceptors(self) -> int

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

def getNumDonors

(

self

)

getNumDonors(self) -> int

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

def getNumExclusions

(

self

)

getNumExclusions(self) -> int

Get the number of donor-acceptor pairs whose interactions should be excluded.

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 getNumPerAcceptorParameters

(

self

)

getNumPerAcceptorParameters(self) -> int

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

def getNumPerDonorParameters

(

self

)

getNumPerDonorParameters(self) -> int

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

def getNumTabulatedFunctions

(

self

)

getNumTabulatedFunctions(self) -> int

Get the number of tabulated functions that have been defined.

def getPerAcceptorParameterName	(		self,
			index
	)

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

Get the name of a per-acceptor parameter.

Parameters:

index

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

Returns:

(string) the parameter name

def getPerDonorParameterName	(		self,
			index
	)

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

Get the name of a per-donor 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 setAcceptorParameters	(		self,
			args
	)

Set the properties of an acceptor group.

Parameters:

index	(int) the index of the acceptor group to set
a1	(int) the index of the first particle for this acceptor group
a2	(int) the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
a3	(int) the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
parameters	(vector< double >) the list of per-acceptor parameter values for the acceptor

def setCutoffDistance	(		self,
			distance
	)

Set the cutoff distance (in nm) being used.

All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters:

distance

(double) the cutoff distance, measured in nm

def setDonorParameters	(		self,
			args
	)

Set the properties of a donor group.

Parameters:

index	(int) the index of the donor group to set
d1	(int) the index of the first particle for this donor group
d2	(int) the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
d3	(int) the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
parameters	(vector< double >) the list of per-donor parameter values for the donor

def setEnergyFunction	(		self,
			energy
	)

Set the algebraic expression that gives the interaction energy between a donor and an acceptor.

def setExclusionParticles	(		self,
			index,
			donor,
			acceptor
	)

Get the donor and acceptor in a pair whose interaction should be excluded.

Parameters:

index	(int) the index of the exclusion for which to get donor and acceptor indices
donor	(int) the index of the donor
acceptor	(int) the index of the acceptor

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 setNonbondedMethod	(		self,
			method
	)

Set the method used for handling long range nonbonded interactions.

def setPerAcceptorParameterName	(		self,
			index,
			name
	)

Set the name of a per-acceptor parameter.

Parameters:

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

def setPerDonorParameterName	(		self,
			index,
			name
	)

Set the name of a per-donor 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-donor and per-acceptor 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 setDonorParameters() and setAcceptorParameters() 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-donor and per-acceptor parameters. All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a donor or acceptor cannot be changed, nor can new donors or acceptors be added.

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:

(bool) true if force uses PBC and false otherwise

Reimplemented from Force.

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Member Data Documentation

CutoffNonPeriodic = _openmm.CustomHbondForce_CutoffNonPeriodic [static]

CutoffPeriodic = _openmm.CustomHbondForce_CutoffPeriodic [static]

NoCutoff = _openmm.CustomHbondForce_NoCutoff [static]

this

Reimplemented from Force.

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

• openmm.py