openmmtools.forces.RadiallySymmetricRestraintForce¶
- class openmmtools.forces.RadiallySymmetricRestraintForce(restraint_parameters, restrained_atom_indices1, restrained_atom_indices2, controlling_parameter_name, *args, **kwargs)[source]¶
Base class for radially-symmetric restraint force.
Provide facility functions to compute the standard state correction of a receptor-ligand restraint.
To create a subclass, implement the properties
restrained_atom_indices1()
andrestrained_atom_indices2()
(with their setters) that return the indices of the restrained atoms.You will also have to implement
_create_bond()
, which should add the bond using the correct function/signature.Optionally, you can implement
distance_at_energy()
if an analytical expression for distance(potential_energy) exists.If you subclass this, and plan on adding additional global parameters, you need to invoke this class
super().__init__
first as thecontrolling_parameter_name
must be the first global variable.- Parameters:
- restraint_parametersOrderedDict
An ordered dictionary containing the bond parameters in the form parameter_name: parameter_value. The order is important to make sure that parameters can be retrieved from the bond force with the correct force index.
- restrained_atom_indices1iterable of int
The indices of the first group of atoms to restrain.
- restrained_atom_indices2iterable of int
The indices of the second group of atoms to restrain.
- controlling_parameter_namestr
The name of the global parameter controlling the energy function.
- *args, **kwargs
Parameters to pass to the super constructor.
- Attributes:
controlling_parameter_name
str: The name of the global parameter controlling the energy function (read-only).
Methods
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
.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.
- __init__(restraint_parameters, restrained_atom_indices1, restrained_atom_indices2, controlling_parameter_name, *args, **kwargs)[source]¶
Methods
__init__
(restraint_parameters, ...)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
.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.
Attributes
controlling_parameter_name
str: The name of the global parameter controlling the energy function (read-only).
restrained_atom_indices1
list: The indices of the first group of restrained atoms.
restrained_atom_indices2
list: The indices of the first group of restrained atoms.
restraint_parameters
OrderedDict: The restraint parameters in dictionary form.