mdadash.backend.analyses.hydrogen_bonds

Number of Hydrogen bonds

Classes

HydrogenBonds()

Number of Hydrogen bonds

class mdadash.backend.analyses.hydrogen_bonds.HydrogenBonds

Bases: WidgetBase

Number of Hydrogen bonds

This widget uses MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis to calculate the number of Hydrogen bonds based on donor, hydrogens and acceptor selections. If donors selection is empty, the Universe topology must contain bonding information. If hydrogens selection or acceptors selection is empty, they are guessed and the Universe must contain charge information for this to work.

Note

It is highly recommended that a universe topology with bond information is used, as this is the only way that guarantees the correct identification of donor-hydrogen pairs.

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

Donor atoms

MDAnalysis selection phrase of donor atoms

Default: name O* N*

Hydrogen atoms

MDAnalysis selection phrase of hydrogen atoms

Default: name H*

Acceptor atoms

MDAnalysis selection phrase of acceptor atoms

Default: name O* N*

d_h_cutoff

Distance cutoff used for finding donor-hydrogen pairs

Default: 1.2

d_a_cutoff

Distance cutoff for hydrogen bonds

Default: 3.0

d_h_a_angle_cutoff

D-H-A angle cutoff for hydrogen bonds, in degrees

Default: 150.0

Update selections

Whether or not to update the selections every frame

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 = 'Number of Hydrogen bonds'

get_parallel_job()

get parallel job handler

name = 'Hydrogen bonds'

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