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

BufferedTrajectory(trajectory, batch_size)	Buffered Trajectory
CommHandler()	Comm Handler
UniverseManager(_wm, _comm_handler)	Universe Manager
WidgetsComm(_um, _wm, _comm_handler)	Widgets Communication

class mdadash.backend.kernel.core.BufferedTrajectory(trajectory: <property object at 0x7d020c19e7f0>, batch_size: int)

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 should be <= 0. trajectory[0] indicates the current frame, trajectory[-1] indicates the previous frame and so on till the configured batch size.

next()

Iterate next frame and copy timestep into buffer

class mdadash.backend.kernel.core.CommHandler

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

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

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)

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

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

Disconnect from MD simulations

init_n_universes(n: int) → None

Initialize array for n universes

Parameters:

n (int) – Number of universes to initialize

pause_simulations(_data: dict) → None

Pause MD simulations

resume_simulations(_data: dict) → None

Resume MD simulations

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

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

Add widget instance based on registered widget name

duplicate_instance(data: dict) → None

Duplicate widget instance based on instance uuid

get_available_widgets(_data: dict)

Send list of available widgets - name and description

get_inputs(data: dict) → list

Get the inputs for a widget instance

remove_instance(data: dict) → dict

Remove widget instance based on uuid

set_input(data: dict) → list

Set an input for a widget instance

mdadash.backend.kernel.core.execute_code(data: dict) → dict

Execute code in this kernel

mdadash.backend.kernel.core.init_n_universes(data: dict) → None

Initialize n universes in UniverseManager