Getting Started

Installation

Using PyPI

The latest version of helanal can be installed from PyPI with:

pip install helanal

From source

To install the current (non-release) version of helanal, you can install the package from source:

pip install git+https://github.com/MDAnalysis/helanal@main

Basic Usage

helanal is used to calculate helix properties for helices with at least 9 residues.

Here, we demonstrate the basic usage and options of helanal. First, import MDAnalysis and helanal:

import MDAnalysis as mda
import helanal

For this example, we will use datafiles from the MDAnalysis tests:

from MDAnalysis.tests.datafiles import PSF, DCD
u = mda.Universe(PSF, DCD)

To analyse a single helix, pass a selection with one atom per residue (normally this will be the Cα atoms):

hel = helanal.HELANAL(u, select='name CA and resnum 161-187')
hel.run()

All computed properties for each simulation frame will be available as arrays in .results, e.g.:

helix_tilt = hel.results.global_tilts

For more details about the properties calculated and method used, see Computed Properties.

Further Options

The simulation frames over which analysis is performed can be specified using start, stop, and/or step, or by providing a list frames with which to slice the trajectory:
```
hel.run(start=5, step=10)
```

The reference axis to which helix tilts and screw angles are calculated can be specified using ref_axis:

hel_xaxis = helanal.HELANAL(u, select='name CA and resnum 161-187',
                            ref_axis=[1,0,0])

To analyse multiple helices at once, pass in a list of selection strings:

hel_multi = helanal.HELANAL(u, select=('name CA and resnum 100-160',
                                       'name CA and resnum 200-230'))

Each property in .results will now be a list of arrays, one for each helix.

By default, the results of a single-helix analysis are flattened, such that each result is a single array, rather than a list-of-arrays of length 1. This behaviour can be turned off (i.e. to be consistent with the behaviour for multi-helix analysis) using flatten_single_helix:
```
hel_noflat = helanal.HELANAL(u, select='name CA and resnum 161-187',
                             flatten_single_helix=False)
```
Analysis can be carried out directly on a single set of positions using the helix_analysis() function:
```
hel_xyz = helanal.helix_analysis(u.atoms.positions, ref_axis=[0, 0, 1])
```
Results are returned as a dictionary.

Citations

helanal is based on the HELANAL algorithm from [Bansal2000], which itself uses the method of [Sugeta1967] to characterise each local axis. Please cite them when using this module in published work.

[Sugeta1967]

Sugeta, H. and Miyazawa, T. 1967. General method for calculating helical parameters of polymer chains from bond lengths, bond angles and internal rotation angles. Biopolymers 5 673 - 679

[Bansal2000]

Bansal M, Kumar S, Velavan R. 2000. HELANAL - A program to characterise helix geometry in proteins. J Biomol Struct Dyn. 17(5):811-819.