adaptivemd.engine package

Subpackages

• adaptivemd.engine.openmm package
  • Submodules
  • adaptivemd.engine.openmm.openmm module
  • adaptivemd.engine.openmm.openmmrun module
  • Module contents

Submodules

adaptivemd.engine.engine module

class adaptivemd.engine.engine.Engine

Bases: adaptivemd.generator.TaskGenerator

An generator for trajectory simulation tasks

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(target, 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

add_output_type(name, filename=None, stride=1, selection=None)

Add an output type for a trajectory kind to be generated by this engine

Parameters:

• name (str) – the name to call the output type by
• filename (str) – a filename to be used for this output type
• stride (int) – the stride used by this particular trajectory relative to the native steps of the engine.
• selection (str) – an mdtraj.Topology.select type filter string to store only a subset of atoms

native_stride

The least common multiple stride of all generated trajectories.

If you want consistent trajectory length your simulation length need to be multiples of this number. The number is relative to the native time steps

Returns:the lcm stride relative to the engines timesteps Return type:int

full_strides

list of strides for trajectories that have full coordinates

this is useful to figure out from which frames you can restart a new trajectory. Usually you only have a single one with full frames.

Returns:the list of strides for full trajectories Return type:list of int

adaptivemd.engine.engine.gcd(a, b)

Return greatest common divisor using Euclid’s Algorithm.

adaptivemd.engine.engine.lcm(a, b)

Return lowest common multiple.

adaptivemd.engine.engine.lcmm(*args)

Return lcm of args.

class adaptivemd.engine.engine.Trajectory(location, frame, length, engine=None)

Bases: adaptivemd.file.File

Represents a trajectory File on the cluster

Variables:

• location (str or File) – the File location
• frame (Frame or File) – the initial frame used for the trajectory
• length (int) – the length of the trajectory in frames
• engine (Engine) – the engine used to create the trajectory

engine

clone()

create a cloned object with equal attributes

Returns:the same type as this object Return type:Location

pick()

Return a random frame from all possible full frames

Returns:the frame you can restart from Return type:Frame

is_folder

file(f)

Return a file location to a file inside the trajectory folder

Parameters:f (str or OutputTypeDescription) – the filename to be appended to the trajectories directory Returns:the object containing the location Return type:File

run()

Return a task to run this engine

Returns:the task object that can be submitted to the queue Return type:Task

extend(length)

Get a task to extend this trajectory if the engine is set

Parameters:length (int or list of int) – the length to extend by as a single int or a list of ints Returns:the task object to extend the trajectory Return type:Task

outputs(outtype)

Get a location to the file containing the output by given name

Parameters:outtype (str or OutputTypeDescription) – the name of the outputtype as str or the full description object Returns:a file location that points to the concrete file that contains the data for a particular output type Return type:File

types

Return the OutputTypeDescriptions for this trajectory

Returns:dict str – the output description dict of the engine Return type:OutputTypeDescription

existing_frames

Returns:a sorted list of frame indices with full coordinates that can be used for restart. relative to the engines timesteps Return type:list of int

class adaptivemd.engine.engine.Frame(trajectory, index)

Bases: adaptivemd.mongodb.base.StorableMixin

Represents a frame of a trajectory

Variables:

• trajectory (Trajectory) – the origin trajectory
• index (int) – the frame index staring from zero

index_in_outputs

Return output type and effective frame index for this frame

Returns:

• str – the name of the output type
• int – the effective index within this trajectory obeying the trajectories own stride

exists

Returns:if True there is a concrete trajectory file with full coordinates for this frame Return type:bool

class adaptivemd.engine.engine.TrajectoryGenerationTask(generator=None, trajectory=None)

Bases: adaptivemd.task.Task

A task that will generate a trajectory

extend(length)

Extend the trajectory that was generated by this task

Parameters:length (int) – the number of frames resp to native engine timesteps Returns:a task to extend the current trajectory Return type:Task

class adaptivemd.engine.engine.TrajectoryExtensionTask(generator=None, trajectory=None, source=None)

Bases: adaptivemd.engine.engine.TrajectoryGenerationTask

A task that generates a trajectory out of a source trajectory

ready

class adaptivemd.engine.engine.OutputTypeDescription(filename=None, stride=1, selection=None)

Bases: adaptivemd.mongodb.base.StorableMixin

A description of a general trajectory type

Variables:

• filename (str) – a filename to store these type of trajectory in
• stride (int) – the stride to be used relative to native engine timesteps
• selection (str) – a mdtraj.Topolopgy.select() like selection of an atom subset

Module contents