nanover.openmm.serializer module

Serialize and deserialize OpenMM simulations to and from XML files.

A simulation is described as the concatenation of a starting structure as a PDB file, an OpenMM serialized system, an OpenMM serialized integrator, and, optionally, an OpenMM serialized state. The resulting XML file looks like:

<OpenMMSimulation>
    <pdbx>
        // pasted content of the PDBx file
    </pdbx>
    <System ...>
        // XML content of the OpenMM serialized system
    </System>
    <Integrator ...>
        // XML content of the OpenMM serialized integrator
    </Integrator>
    <State>
        // XML content of the OpenMM serialized state
    </State>
</OpenMMSimulation>

The System, Integrator and State tags are the roots of the serialized system, integrator and state, respectively. The pdbx tag can be replaced by a

pdb one for backward compatibility.

This module provides a function serialize_simulation() that generates an XML file from an existing instance of openmm.app.Simulation, and a function deserialize_simulation() that creates an instance of simulation from an XML file.

nanover.openmm.serializer.deserialize_simulation(xml_content: str | TextIO, imd_force: CustomExternalForce | None = None, platform_name: str | None = None, ignore_state=False) → Simulation

Create an OpenMM simulation from XML.

Parameters:

• xml_content – The content of an XML file as a string.

• imd_force – Optionally, an imd force to populate and add to the system. The force must be created by nanover.openmm.potentials.create_imd_force().

• ignore_state – Ignore serialized state when present

Returns:

An instance of the simulation.

nanover.openmm.serializer.serialize_simulation(simulation: Simulation, save_state=False) → str

Generate an XML string from a simulation.

Parameters:

• simulation – The simulation to serialize.

• save_state – Save the present state of the simulation too.

Returns:

A string with the content of an XML file describing the simulation.