narupa.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>
</OpenMMSimulation>

The System and Integrator tags are the roots of the serialized system and integrator, 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 simtk.openmm.app.Simulation, and a function deserialize_simulation() that creates an instance of simulation from an XML file.

narupa.openmm.serializer.deserialize_simulation(xml_content: str, imd_force: Optional[pretends.CustomExternalForce] = None) → pretends.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 narupa.openmm.potentials.create_imd_force().

Returns:

An instance of the simulation.

narupa.openmm.serializer.serialize_simulation(simulation: pretends.Simulation) → str

Generate an XML string from a simulation.

Parameters:simulation – The simulation to serialize. Returns:A string with the content of an XML file describing the simulation.