mdadash.backend.analyses.rmsd

RMSD Analysis

Classes

RMSD()

RMSD Analysis

class mdadash.backend.analyses.rmsd.RMSD

Bases: WidgetBase

RMSD Analysis

This widget uses MDAnalysis.analysis.rms.rmsd to calculate RMSD of a selection. The reference positions used by this widget are the initial positions of the selection available for the trajectory from the reference timestep (ref_u).

Note

If you use trajectory data from simulations performed under periodic boundary conditions then you must make your molecules whole before performing RMSD calculations so that the centers of mass of the mobile and reference structure are properly superimposed.

You can add custom transformations to the universe in the Universe Configuration section in the Settings page of the dasboard.

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: protein

Center

Subtract center of geometry before calculation

Default: False

Superposition:

Perform a rotational and translational superposition with the fast QCP algorithm

Default: False

Weights:

Weights to use to compute weighted average.

One of None, masses, charges, Custom function

Default: None

Custom weights function:

Name of the custom weights function to use to obtain weights. This is applicable only when the Weights input above is set to Custom function.

A custom function can be defined using the Notebook interface. The function should take one parameter (MDAnalysis AtomGroup) as input and should return a 1D array of weights of the same length as the passed in selection AtomGroup.

Example:

import numpy as np

def rmsd_custom_weights_function(ag):
    return np.sqrt(ag.masses)

Default: ‘’

Custom title

Custom title for the plot

Default: ‘’

Max values

Max values to show in plot

Default: 100

Plot refresh frequency

The frequency with which the plot is refreshed (every n frames). This only applies when the run frequency is every-frame

Default: 1

Reset on connect

Reset the plot on every connect

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 = 'RMSD of a selection'

get_parallel_job()

get_parallel_job() handler

name = 'RMSD'

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