openmmtools.forces.RadiallySymmetricRestraintForce

class openmmtools.forces.RadiallySymmetricRestraintForce(restraint_parameters, restrained_atom_indices1, restrained_atom_indices2, controlling_parameter_name, *args, **kwargs)

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() and restrained_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 the controlling_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)

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.