mdadash.backend.analyses.com_distance

Distance between two center-of-masses

Classes

COMDistance()

COM Distance

class mdadash.backend.analyses.com_distance.COMDistance

Bases: WidgetBase

COM Distance

This widget shows the distance between two center-of-masses (COMs).

Inputs

Run frequency

The frequency with which the widget is run - every-frame or batch

Default: every-frame

Run mode

The mode in which the widget is run - serial or parallel

Default: serial

Selection 1

First MDAnalysis selection phrase

Default: protein

Selection 2

Second MDAnalysis selection phrase

Default: resid 1

Periodic

Select with periodic boundary conditions

Default: True

Updating

Update selection during each timestep

Default: False

Custom title

Custom title for the plot

Default: ‘’

Max values

Max values to show in plot

Default: 100

Max distance

Max distance for alert check

Default: 50.0

Alert if distance > ‘Max distance

Create an alert if the above condition is met

Default: False

Pause simulation if distance > ‘Max distance’

Pause the simulation if the above condition is met

Default: False

X-axis

X-axis value - time or step

Default: time

Output

Here is an example output plot of this widget:

Tip

This widget supports batching and can run in parallel

apply_parallel_results(values)

apply_parallel_results() handler

description = 'Distance between two COMs'

get_parallel_job()

get_parallel_job() handler

name = 'COMDistance'

on_input_change(attribute, _old_value, new_value)

on_input_change() handler

on_post_connect()

on_post_connect() handler

on_post_create()

on_post_create() handler

run_batch()

run_batch() handler

run_every_frame()

run_every_frame() handler