mdadash.backend.kernel.core

Kernel core where MDAnalysis code runs

Functions

`execute_code`(data)	Execute code in this kernel
`init_n_universes`(data)	Initialize n universes in `UniverseManager`

Classes

`BufferFrameIteratorIndices`(trajectory, frames)	Iterable over the frames of a trajectory buffer listed as a sequence of indices.
`BufferedTrajectory`(trajectory, buffer_size)	Buffered Trajectory
`CommHandler`()	Comm Handler
`UniverseManager`(_wm, _comm_handler)	Universe Manager
`WidgetsComm`(_um, _wm, _comm_handler)	Widgets Communication

class mdadash.backend.kernel.core.BufferFrameIteratorIndices(trajectory, frames)[source]

Bases: FrameIteratorBase

Iterable over the frames of a trajectory buffer listed as a sequence of indices. This is very similar to FrameIteratorIndices in MDAnalysis, but without rewind() and __getitem__ as they aren’t needed here.

property frames

class mdadash.backend.kernel.core.BufferedTrajectory(trajectory: <property object at 0x75ac43b54770>, buffer_size: int)[source]

Bases: object

Buffered Trajectory

This class is a wrapper for the trajectory reader and provides buffered access to the last n timesteps.

trajectory[index] can be used to access individual frames. Index values can range from 0 to the configured batch size.

property buffer_size

check_slice_indices(start, stop, step)[source]

property n_frames

next()[source]: Iterate next frame and copy timestep into buffer

class mdadash.backend.kernel.core.CommHandler[source]

Bases: object

Comm Handler

This class is responsible for handling all the communication to and from this kernel. This is the class that interfaces with the KernelManager on the server side.

register_handler(msg_type: str, handler_func: callable) → None[source]

Register a handler function for a message type

Parameters:

msg_type (str) – A message type to identify the handler
handler_func (callable) – The handler function to invoke when a message with this message type is received

send(msg: dict) → None[source]

Send a message (response) back on the comm

Parameters:: msg (dict) – A generic message dictionary

class mdadash.backend.kernel.core.UniverseManager(_wm: WidgetManager, _comm_handler: CommHandler)[source]

Bases: object

Universe Manager

This class is responsible for managing all MDAnalysis universes. It has handlers to interact with the MD simulation. These handlers are invoked by comm messages sent from the server.

This also provides an iterable and indexable access to the individual universes.

connect_to_simulations(universe_configs: list[dict]) → None[source]

Connect to MD simulations

Parameters:: universe_configs (list[dict]) – A list of configurations for universe(s) creation. Each dict has universe related config like topology, trajectory, imdclient params, user-defined kwargs etc

disconnect_from_simulations(_data: dict) → None[source]: Disconnect from MD simulations

init_n_universes(n: int) → None[source]

Initialize array for n universes

Parameters:: n (int) – Number of universes to initialize

pause_simulations(_data: dict) → None[source]: Pause MD simulations

resume_simulations(_data: dict) → None[source]: Resume MD simulations

class mdadash.backend.kernel.core.WidgetsComm(_um: UniverseManager, _wm: WidgetManager, _comm_handler: CommHandler)[source]

Bases: object

Widgets Communication

This class is responsible for handling communications related to widgets. It uses WidgetManager instance and communicates via CommHandler back to the server from this kernel.

add_instance(data: dict) → dict[source]: Add widget instance based on registered widget name

duplicate_instance(data: dict) → None[source]: Duplicate widget instance based on instance uuid

get_available_widgets(_data: dict)[source]: Send list of available widgets - name and description

get_inputs(data: dict) → list[source]: Get the inputs for a widget instance

recreate_instances(data: dict) → dict[source]: Recreate widget instances from state file

remove_instance(data: dict) → dict[source]: Remove widget instance based on uuid

set_input(data: dict) → list[source]: Set an input for a widget instance

mdadash.backend.kernel.core.execute_code(data: dict) → dict[source]: Execute code in this kernel

mdadash.backend.kernel.core.init_n_universes(data: dict) → None[source]: Initialize n universes in UniverseManager