mdadash.backend.analyses.helix_analysis

Helix Analysis

Classes

HelixAnalysis()

Helix Analysis

class mdadash.backend.analyses.helix_analysis.HelixAnalysis

Bases: WidgetBase

Helix Analysis

This widget uses MDAnalysis.analysis.helix_analysis.HELANAL to perform Helix analysis and plot different computed properties.

Plots can be chosen for the following computed properties:

• local_twists

• local_nres_per_turn

• local_bends

• local_heights

• local_screw_angles

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

MDAnalysis selection phrase

Default: resid 1:10 and name CA

Note

HELANAL is designed to work on the alpha-carbon atoms of protein residues and the selection must return at least 9 residues

Property

Computed property to plot

Default: local_twists

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 = 'Helix analysis using HELANAL'

get_parallel_job()

get parallel job handler

name = 'Helix Analysis'

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