openmmtools.forces.RadiallySymmetricBondRestraintForce

class openmmtools.forces.RadiallySymmetricBondRestraintForce(energy_function, restraint_parameters, restrained_atom_index1, restrained_atom_index2, controlling_parameter_name='lambda_restraints')[source]

Base class for radially-symmetric restraints between two atoms.

This is a version of RadiallySymmetricCentroidRestraintForce that can be used with OpenCL 32-bit platforms. It supports atom groups with only a single atom.

Attributes:
controlling_parameter_name

str: The name of the global parameter controlling the energy function (read-only).

restrained_atom_indices1

The indices of the first group of restrained atoms.

restrained_atom_indices2

The indices of the first group of restrained atoms.

restraint_parameters

OrderedDict: The restraint parameters in dictionary form.

Methods

addBond(self, particle1, particle2, parameters) addBond(self, particle1, particle2) -> int
addEnergyParameterDerivative(self, name) Request that this Force compute the derivative of its energy with respect to a global parameter.
addGlobalParameter(self, name, defaultValue) Add a new global parameter that the interaction may depend on.
addPerBondParameter(self, name) Add a new per-bond parameter that the interaction may depend on.
compute_standard_state_correction(…[, …]) Return the standard state correction of the restraint.
deserialize_xml(xml_serialization) Shortcut to deserialize the XML representation and the restore interface.
distance_at_energy(potential_energy) Compute the distance at which the potential energy is potential_energy.
getBondParameters(self, index) Get the force field parameters for a bond term.
getEnergyFunction(self) Get the algebraic expression that gives the interaction energy for each bond
getEnergyParameterDerivativeName(self, index) Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getForceGroup(self) Get the force group this Force belongs to.
getGlobalParameterDefaultValue(self, index) Get the default value of a global parameter.
getGlobalParameterName(self, index) Get the name of a global parameter.
getNumBonds(self) Get the number of bonds for which force field parameters have been defined.
getNumEnergyParameterDerivatives(self) Get the number of global parameters with respect to which the derivative of the energy should be computed.
getNumGlobalParameters(self) Get the number of global parameters that the interaction depends on.
getNumPerBondParameters(self) Get the number of per-bond parameters that the interaction depends on.
getPerBondParameterName(self, index) Get the name of a per-bond parameter.
is_restorable(openmm_object) Check if the custom integrator or force has a restorable interface.
restore_interface(openmm_object) Restore the original interface of an OpenMM custom force or integrator.
setBondParameters(self, index, particle1, …) Set the force field parameters for a bond term.
setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy for each bond
setForceGroup(self, group) Set the force group this Force belongs to.
setGlobalParameterDefaultValue(self, index, …) Set the default value of a global parameter.
setGlobalParameterName(self, index, name) Set the name of a global parameter.
setPerBondParameterName(self, index, name) Set the name of a per-bond parameter.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-bond parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions(self) Returns whether or not this force makes use of periodic boundary conditions.
__init__(self, energy) → CustomBondForce[source]

__init__(self, other) -> CustomBondForce

Create a CustomBondForce.

Parameters:
energy : string

an algebraic expression giving the interaction energy between two bonded particles as a function of r, the distance between them

Methods

__init__(self, energy) __init__(self, other) -> CustomBondForce
addBond(self, particle1, particle2, parameters) addBond(self, particle1, particle2) -> int
addEnergyParameterDerivative(self, name) Request that this Force compute the derivative of its energy with respect to a global parameter.
addGlobalParameter(self, name, defaultValue) Add a new global parameter that the interaction may depend on.
addPerBondParameter(self, name) Add a new per-bond parameter that the interaction may depend on.
compute_standard_state_correction(…[, …]) Return the standard state correction of the restraint.
deserialize_xml(xml_serialization) Shortcut to deserialize the XML representation and the restore interface.
distance_at_energy(potential_energy) Compute the distance at which the potential energy is potential_energy.
getBondParameters(self, index) Get the force field parameters for a bond term.
getEnergyFunction(self) Get the algebraic expression that gives the interaction energy for each bond
getEnergyParameterDerivativeName(self, index) Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getForceGroup(self) Get the force group this Force belongs to.
getGlobalParameterDefaultValue(self, index) Get the default value of a global parameter.
getGlobalParameterName(self, index) Get the name of a global parameter.
getNumBonds(self) Get the number of bonds for which force field parameters have been defined.
getNumEnergyParameterDerivatives(self) Get the number of global parameters with respect to which the derivative of the energy should be computed.
getNumGlobalParameters(self) Get the number of global parameters that the interaction depends on.
getNumPerBondParameters(self) Get the number of per-bond parameters that the interaction depends on.
getPerBondParameterName(self, index) Get the name of a per-bond parameter.
is_restorable(openmm_object) Check if the custom integrator or force has a restorable interface.
restore_interface(openmm_object) Restore the original interface of an OpenMM custom force or integrator.
setBondParameters(self, index, particle1, …) Set the force field parameters for a bond term.
setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy for each bond
setForceGroup(self, group) Set the force group this Force belongs to.
setGlobalParameterDefaultValue(self, index, …) Set the default value of a global parameter.
setGlobalParameterName(self, index, name) Set the name of a global parameter.
setPerBondParameterName(self, index, name) Set the name of a per-bond parameter.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-bond parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions(self) Returns whether or not this force makes use of periodic boundary conditions.

Attributes

controlling_parameter_name str: The name of the global parameter controlling the energy function (read-only).
restrained_atom_indices1 The indices of the first group of restrained atoms.
restrained_atom_indices2 The indices of the first group of restrained atoms.
restraint_parameters OrderedDict: The restraint parameters in dictionary form.
addBond(self, particle1, particle2, parameters) → int

addBond(self, particle1, particle2) -> int

Add a bond term to the force field.

Parameters:
particle1 : int

the index of the first particle connected by the bond

particle2 : int

the index of the second particle connected by the bond

parameters : vector< double >

the list of parameters for the new bond

Returns:
int

the index of the bond that was added

addEnergyParameterDerivative(self, name)

Request that this Force compute the derivative of its energy with respect to a global parameter. The parameter must have already been added with addGlobalParameter().

Parameters:
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:
int

the index of the parameter that was added

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

compute_standard_state_correction(thermodynamic_state, square_well=False, radius_cutoff=None, energy_cutoff=None, max_volume=None)

Return the standard state correction of the restraint.

The standard state correction is computed as

  • log(V_standard / V_restraint)

where V_standard is the volume at standard state concentration and V_restraint is the restraint volume. V_restraint is bounded by the volume of the periodic box.

The square_well parameter, can be used to re-compute the standard state correction when removing the bias introduced by the restraint.

Parameters:
thermodynamic_state : states.ThermodynamicState

The thermodynamic state at which to compute the standard state correction.

square_well : bool, optional

If True, this computes the standard state correction assuming the restraint to obey a square well potential. The energy cutoff is still applied to the original energy potential.

radius_cutoff : simtk.unit.Quantity, optional

The maximum distance achievable by the restraint (units compatible with nanometers). This is equivalent to placing a hard wall potential at this distance.

energy_cutoff : float, optional

The maximum potential energy achievable by the restraint in kT. This is equivalent to placing a hard wall potential at a distance such that potential_energy(distance) == energy_cutoff.

max_volume : simtk.unit.Quantity or ‘system’, optional

The volume of the periodic box (units compatible with nanometer**3). This must be provided the thermodynamic state is in NPT. If the string ‘system’ is passed, the maximum volume is computed from the system box vectors (this has no effect if the system is not periodic).

Returns:
correction : float

The unit-less standard state correction in kT at the given thermodynamic state.

Raises:
TypeError

If the thermodynamic state is in the NPT ensemble, and max_volume is not provided, or if the system is non-periodic and no cutoff is given.

controlling_parameter_name

str: The name of the global parameter controlling the energy function (read-only).

classmethod deserialize_xml(xml_serialization)

Shortcut to deserialize the XML representation and the restore interface.

Parameters:
xml_serialization : str

The XML representation of the OpenMM custom force/integrator.

Returns:
openmm_object

The deserialized OpenMM force/integrator with the original interface restored (if restorable).

distance_at_energy(potential_energy)

Compute the distance at which the potential energy is potential_energy.

Parameters:
potential_energy : simtk.unit.Quantity

The potential energy of the restraint (units of energy/mole).

Returns:
distance : simtk.unit.Quantity

The distance at which the potential energy is potential_energy (units of length).

getBondParameters(self, index)

Get the force field parameters for a bond term.

Parameters:
index : int

the index of the bond for which to get parameters

Returns:
particle1 : int

the index of the first particle connected by the bond

particle2 : int

the index of the second particle connected by the bond

parameters : vector< double >

the list of parameters for the bond

getEnergyFunction(self) → std::string const &

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

getEnergyParameterDerivativeName(self, index) → std::string const &

Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.

Parameters:
index : int

the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives()

Returns:
string

the parameter name

getForceGroup(self) → int

Get the force group this Force belongs to.

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

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

getNumBonds(self) → int

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

getNumEnergyParameterDerivatives(self) → int

Get the number of global parameters with respect to which the derivative of the energy should be computed.

getNumGlobalParameters(self) → int

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

getNumPerBondParameters(self) → int

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

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

classmethod is_restorable(openmm_object)

Check if the custom integrator or force has a restorable interface.

Parameters:
openmm_object : object

The custom integrator or force to check.

Returns:
True if the object has a restorable interface, False otherwise.
classmethod restore_interface(openmm_object)

Restore the original interface of an OpenMM custom force or integrator.

The function restore the methods of the original class that inherited from RestorableOpenMMObject. Return False if the interface could not be restored.

Parameters:
openmm_object : object

The object to restore.

Returns:
True if the original class interface could be restored, False otherwise.
restrained_atom_indices1

The indices of the first group of restrained atoms.

restrained_atom_indices2

The indices of the first group of restrained atoms.

restraint_parameters

OrderedDict: The restraint parameters in dictionary form.

setBondParameters(self, index, particle1, particle2, parameters) setBondParameters(self, index, particle1, particle2)

Set the force field parameters for a bond term.

Parameters:
index : int

the index of the bond for which to set parameters

particle1 : int

the index of the first particle connected by the bond

particle2 : int

the index of the second particle connected by the bond

parameters : vector< double >

the list of parameters for the bond

setEnergyFunction(self, energy)

Set the algebraic expression that gives the interaction energy for each bond

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).

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

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

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

setUsesPeriodicBoundaryConditions(self, periodic)

Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

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.

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