adaptivemd.engine.openmm package

Submodules

adaptivemd.engine.openmm.openmm module

class adaptivemd.engine.openmm.openmm.OpenMMEngine(system_file, integrator_file, pdb_file, args=None)[source]

Bases: adaptivemd.engine.engine.Engine

OpenMM Engine to be used by Adaptive MD

Variables:
  • system_file (File) – the system.xml file for OpenMM
  • integrator_file (File) – the integrator.xml file for OpenMM
  • pdb_file (File) – the .pdb file for the topology
  • args (str) – a list of arguments passed to the openmmrun.py script
classmethod from_dict(dct)[source]

Reconstruct an object from a dictionary representation

Parameters:dct (dict) – the dictionary containing a state representation of the class.
Returns:the reconstructed storable object
Return type:StorableMixin
to_dict()[source]

Convert object into a dictionary representation

Used to convert the dictionary into JSON string for serialization

Returns:the dictionary representing the (immutable) state of the object
Return type:dict
static then_func_import(project, task, data, inputs)[source]
run(target)[source]

Create a task that returns a trajectory given in the input

Parameters:target (Trajectory) – location of the created target trajectory
Returns:the task object containing the job description
Return type:Task
extend(source, length)[source]

Create a task that extends a trajectory given in the input

Parameters:
  • target (Trajectory) – location of the target trajectory to be extended
  • length (int) – number of additional frames to be computed
Returns:

the task object containing the job description
Return type:

Task

adaptivemd.engine.openmm.openmmrun module

Module contents