openmmtools.testsystems.TestSystem¶
- class openmmtools.testsystems.TestSystem(**kwargs)[source]¶
Abstract base class for test systems, demonstrating how to implement a test system.
- Parameters:
Notes
Unimplemented methods will default to the base class methods, which raise a NotImplementedException.
Examples
Create a test system.
>>> testsystem = TestSystem()
Retrieve a deep copy of the System object.
>>> system = testsystem.system
Retrieve a deep copy of the positions.
>>> positions = testsystem.positions
Retrieve a deep copy of the topology.
>>> topology = testsystem.topology
Serialize system and positions to XML (to aid in debugging).
>>> (system_xml, positions_xml) = testsystem.serialize()
- Attributes:
system
openmm.SystemThe openmm.System object corresponding to the test system.
positions
listThe openmm.unit.Quantity object containing the particle positions, with units compatible with openmm.unit.nanometers.
topology
listThe openmm.app.Topology object corresponding to the test system.
Methods
reduced_potential_expectation
(...)Calculate the expected potential energy in state_sampled_from, divided by kB * T in state_evaluated_in.
serialize
()Return the System and positions in serialized XML form.
Methods
__init__
(**kwargs)Abstract base class for test system.
reduced_potential_expectation
(...)Calculate the expected potential energy in state_sampled_from, divided by kB * T in state_evaluated_in.
serialize
()Return the System and positions in serialized XML form.
Attributes
analytical_properties
A list of available analytical properties, accessible via 'get_propertyname(thermodynamic_state)' calls.
mdtraj_topology
The mdtraj.Topology object corresponding to the test system (read-only).
name
The name of the test system.
positions
The openmm.unit.Quantity object containing the particle positions, with units compatible with openmm.unit.nanometers.
system
The openmm.System object corresponding to the test system.
topology
The openmm.app.Topology object corresponding to the test system.