mdadash.backend.analyses.contacts

Contacts within a cutoff

Classes

Contacts()

Contacts within a cutoff

class mdadash.backend.analyses.contacts.Contacts

Bases: WidgetBase

Contacts within a cutoff

This widget uses MDAnalysis.lib.distances.capped_distance to caclulate number of contacts within a cutoff between two contacting groups.

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

Contacting Group 1

MDAnalysis selection phrase of first group

Default: (resname ASP GLU) and (name OE* OD*)

Contacting Group 2

MDAnalysis selection phrase of second group

Default: (resname ARG LYS) and (name NH* NZ)

Radius

Radius within which contacts exist

Default: 4.5

Custom title

Custom title for the plot

Default: ‘’

Max values

Max values to show in plot

Default: 100

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 = 'Contacts within a cutoff'

get_parallel_job()

get parallel job handler

name = 'Contacts'

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()

batch run handler

run_every_frame()

every-frame run handler