adaptivemd.OpenMMEngine

class adaptivemd.OpenMMEngine(system_file, integrator_file, pdb_file, args=None)

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

__init__(system_file, integrator_file, pdb_file, args=None)

x.__init__(…) initializes x; see help(type(x)) for signature

Methods

__init__(system_file, integrator_file, pdb_file)	x.__init__(…) initializes x; see help(type(x)) for signature
add_output_type(name[, filename, stride, …])	Add an output type for a trajectory kind to be generated by this engine
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableMixin
descendants()	Return a list of all subclassed objects
extend(source, length)	Create a task that extends a trajectory given in the input
from_dict(dct)	Reconstruct an object from a dictionary representation
get_uuid()	Create a new unique ID :returns: the unique number for an object in the project :rtype: long
idx(store)	Return the index which is used for the object in the given store.
items()
named(name)	Attach a .name property to an object
objects()	Returns a dictionary of all storable objects
run(target)	Create a task that returns a trajectory given in the input
stage(obj[, target])	Short cut to add a file to be staged
then_func_import(project, task, data, inputs)
to_dict()	Convert object into a dictionary representation

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
cls	Return the class name as a string
files
full_strides	list of strides for trajectories that have full coordinates
native_stride	The least common multiple stride of all generated trajectories.
stage_in	Return a list of actions needed before tasks can be generated

classmethod from_dict(dct)

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()

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

run(target)

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)

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