openmmtools.testsystems.TestSystem¶

class openmmtools.testsystems.TestSystem(**kwargs)[source]¶

Abstract base class for test systems, demonstrating how to implement a test system.

Parameters:

Attributes:

systemopenmm.System: The openmm.System object corresponding to the test system.
positionslist: The openmm.unit.Quantity object containing the particle positions, with units compatible with openmm.unit.nanometers.
topologylist: The 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.

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()

__init__(**kwargs)[source]¶

Abstract base class for test system.

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.

openmmtools