mdadash.backend.analyses.native_contacts

Native Contacts Analysis

Classes

NativeContacts()

Native Contacts Analysis

class mdadash.backend.analyses.native_contacts.NativeContacts

Bases: WidgetBase

Native Contacts Analysis

This widget uses MDAnalysis.analysis.contacts.Contacts to calculate Fraction of native contacts between two contacting groups.

Note

The two contacting AtomGroups in their reference conformation are created when this widget instance is created or whenever the inputs for the above Class from below are updated.

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: protein and name CA

Contacting Group 2

MDAnalysis selection phrase of second group

Default: protein and name CA

Radius

Radius within which contacts exist in refgroup

Default: 4.5

Method

Method to use for cut off - hard_cut, soft_cut or radius_cut

Default: hard_cut

PBC

Uses periodic boundary conditions to calculate distances

Default: True

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 = 'Native Contacts Analysis'

get_parallel_job()

get parallel job handler

name = 'Native 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