CustomHbondForce

class simtk.openmm.openmm.CustomHbondForce(*args)

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.

__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

Methods

__init__((self, energy) -> CustomHbondForce) __init__(self, other) -> CustomHbondForce
addAcceptor((self, a1, a2, a3, ...) addAcceptor(self, a1, a2, a3) -> int
addDonor((self, d1, d2, d3, parameters) -> int) addDonor(self, d1, d2, d3) -> int
addExclusion((self, donor, acceptor) -> int) Add a donor-acceptor pair to the list of interactions that should be excluded.
addFunction((self, name, values, min, ...) Add a tabulated function that may appear in the energy expression.
addGlobalParameter((self, name, ...) Add a new global parameter that the interaction may depend on.
addPerAcceptorParameter((self, name) -> int) Add a new per-acceptor parameter that the interaction may depend on.
addPerDonorParameter((self, name) -> int) Add a new per-donor parameter that the interaction may depend on.
addTabulatedFunction((self, name, ...) Add a tabulated function that may appear in the energy expression.
getAcceptorParameters(self, index) Get the properties of an acceptor group.
getCutoffDistance((self) -> double) Get the cutoff distance (in nm) being used.
getDonorParameters(self, index) Get the properties of a donor group.
getEnergyFunction((self) -> std::string const &) Get the algebraic expression that gives the interaction energy between a donor and an acceptor
getExclusionParticles(self, index) Get the donor and acceptor in a pair whose interaction should be excluded.
getForceGroup((self) -> int) Get the force group this Force belongs to.
getFunctionParameters(self, index) Get the parameters for a tabulated function that may appear in the energy expression.
getGlobalParameterDefaultValue((self, ...) Get the default value of a global parameter.
getGlobalParameterName((self, ...) Get the name of a global parameter.
getNonbondedMethod(...) Get the method used for handling long range nonbonded interactions.
getNumAcceptors((self) -> int) Get the number of acceptors for which force field parameters have been defined.
getNumDonors((self) -> int) Get the number of donors for which force field parameters have been defined.
getNumExclusions((self) -> int) Get the number of donor-acceptor pairs whose interactions should be excluded.
getNumFunctions((self) -> int) Get the number of tabulated functions that have been defined.
getNumGlobalParameters((self) -> int) Get the number of global parameters that the interaction depends on.
getNumPerAcceptorParameters((self) -> int) Get the number of per-acceptor parameters that the interaction depends on.
getNumPerDonorParameters((self) -> int) Get the number of per-donor parameters that the interaction depends on.
getNumTabulatedFunctions((self) -> int) Get the number of tabulated functions that have been defined.
getPerAcceptorParameterName((self, ...) Get the name of a per-acceptor parameter.
getPerDonorParameterName((self, ...) Get the name of a per-donor parameter.
getTabulatedFunction((self, ...) getTabulatedFunction(self, index) -> TabulatedFunction
getTabulatedFunctionName((self, ...) Get the name of a tabulated function that may appear in the energy expression.
setAcceptorParameters(self, index, a1, a2, ...) setAcceptorParameters(self, index, a1, a2, a3)
setCutoffDistance(self, distance) Set the cutoff distance (in nm) being used.
setDonorParameters(self, index, d1, d2, d3, ...) setDonorParameters(self, index, d1, d2, d3)
setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy between a donor and an acceptor
setExclusionParticles(self, index, donor, ...) Get the donor and acceptor in a pair whose interaction should be excluded.
setForceGroup(self, group) Set the force group this Force belongs to.
setFunctionParameters(self, index, name, ...) Set the parameters for a tabulated function that may appear in the energy expression.
setGlobalParameterDefaultValue(self, index, ...) Set the default value of a global parameter.
setGlobalParameterName(self, index, name) Set the name of a global parameter.
setNonbondedMethod(self, method) Set the method used for handling long range nonbonded interactions.
setPerAcceptorParameterName(self, index, name) Set the name of a per-acceptor parameter.
setPerDonorParameterName(self, index, name) Set the name of a per-donor parameter.
updateParametersInContext(self, context) Update the per-donor and per-acceptor parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.

Attributes

CutoffNonPeriodic
CutoffPeriodic
NoCutoff
getNumDonors(self) → int

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

getNumAcceptors(self) → int

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

getNumExclusions(self) → int

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

getNumPerDonorParameters(self) → int

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

getNumPerAcceptorParameters(self) → int

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

getNumGlobalParameters(self) → int

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

getNumTabulatedFunctions(self) → int

Get the number of tabulated functions that have been defined.

getNumFunctions(self) → int

Get the number of tabulated functions that have been defined.

Deprecated

This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
getEnergyFunction(self) → std::string const &

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

setEnergyFunction(self, energy)

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

getNonbondedMethod(self) → OpenMM::CustomHbondForce::NonbondedMethod

Get the method used for handling long range nonbonded interactions.

setNonbondedMethod(self, method)

Set the method used for handling long range nonbonded interactions.

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:the cutoff distance, measured in nm
Return type:double
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
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:the index of the parameter that was added
Return type:int
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:the parameter name
Return type:string
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
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:the index of the parameter that was added
Return type:int
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:the parameter name
Return type:string
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
addGlobalParameter(self, name, defaultValue) → int

Add a new global parameter that the interaction may depend on. The default value provided to this method is the initial value of the parameter in newly created Contexts. You can change the value at any time by calling setParameter() on the Context.

Parameters:
  • name (string) – the name of the parameter
  • defaultValue (double) – the default value of the parameter
Returns:

the index of the parameter that was added

Return type:

int

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:the parameter name
Return type:string
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
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:the parameter default value
Return type:double
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
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:

the index of the donor that was added

Return type:

int

getDonorParameters(self, index)

Get the properties of a donor group.

Parameters:index (int) – the index of the donor group to get
Returns:
  • 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 will be -1.
  • d3 (int) – the index of the third particle for this donor group. If the group includes less than three particles, this will be -1.
  • parameters (vector< double >) – the list of per-donor parameter values for the donor
setDonorParameters(self, index, d1, d2, d3, parameters)

setDonorParameters(self, index, d1, d2, d3)

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
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:

the index of the acceptor that was added

Return type:

int

getAcceptorParameters(self, index)

Get the properties of an acceptor group.

Parameters:index (int) – the index of the acceptor group to get
Returns:
  • 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 will be -1.
  • a3 (int) – the index of the third particle for this acceptor group. If the group includes less than three particles, this will be -1.
  • parameters (vector< double >) – the list of per-acceptor parameter values for the acceptor
setAcceptorParameters(self, index, a1, a2, a3, parameters)

setAcceptorParameters(self, index, a1, a2, a3)

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
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:

the index of the exclusion that was added

Return type:

int

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:
  • donor (int) – the index of the donor
  • acceptor (int) – the index of the acceptor
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
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:

the index of the function that was added

Return type:

int

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:the TabulatedFunction object defining the function
Return type:TabulatedFunction
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:the name of the function as it appears in expressions
Return type:string
addFunction(self, name, values, min, max) → int

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

Deprecated

This method exists only for backward compatibility. Use addTabulatedFunction() instead.
getFunctionParameters(self, index)

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

Deprecated

This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead. If the specified function is not a Continuous1DFunction, this throws an exception.
setFunctionParameters(self, index, name, values, min, max)

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

Deprecated

This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead. If the specified function is not a Continuous1DFunction, this throws an exception.
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.

usesPeriodicBoundaryConditions(self) → bool

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

Returns:true if force uses PBC and false otherwise
Return type:bool
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).