MembraneCurvature

Author:

Estefania Barreto-Ojeda

Year:

2021

Copyright:

GNU Public License v3

MembraneCurvature calculates the mean and Gaussian curvature of surfaces derived from a selection of reference.

Mean curvature is calculated in units of Å -1 and Gaussian curvature in units of Å -2.

class membrane_curvature.base.MembraneCurvature(universe, select='all', n_x_bins=100, n_y_bins=100, x_range=None, y_range=None, wrap=True, **kwargs)[source]

MembraneCurvature is a tool to calculate membrane curvature.

Parameters:

  • universe (Universe or AtomGroup) – An MDAnalysis Universe object.

  • select (str or iterable of str, optional.) – The selection string of an atom selection to use as a reference to derive a surface.

  • wrap (bool, optional) – Apply coordinate wrapping to pack atoms into the primary unit cell.

  • n_x_bins (int, optional, default: ‘100’) – Number of bins in grid in the x dimension.

  • n_y_bins (int, optional, default: ‘100’) – Number of bins in grid in the y dimension.

  • x_range (tuple of (float, float), optional, default: (0, universe.dimensions[0])) – Range of coordinates (min, max) in the x dimension.

  • y_range (tuple of (float, float), optional, default: (0, universe.dimensions[1])) – Range of coordinates (min, max) in the y dimension.

Variables:

  • results.z_surface (ndarray) – Surface derived from atom selection in every frame. Array of shape (n_frames, n_x_bins, n_y_bins)

  • results.mean (ndarray) – Mean curvature associated to the surface. Array of shape (n_frames, n_x_bins, n_y_bins)

  • results.gaussian (ndarray) – Gaussian curvature associated to the surface. Arrays of shape (n_frames, n_x_bins, n_y_bins)

  • results.average_z_surface (ndarray) – Average of the array elements in z_surface. Each array has shape (n_x_bins, n_y_bins)

  • results.average_mean (ndarray) – Average of the array elements in mean_curvature. Each array has shape (n_x_bins, n_y_bins)

  • results.average_gaussian (ndarray) – Average of the array elements in gaussian_curvature. Each array has shape (n_x_bins, n_y_bins)

See also

wrap

Wrap/unwrap the atoms of a given AtomGroup in the unit cell.

Notes

Use wrap=True to translates the atoms of your mda.Universe back in the unit cell. Use wrap=False for processed trajectories where rotational/translational fit is performed.

For more details on when to use wrap=True, check the Usage page.

The derived surface and calculated curvatures are available in the results attributes.

The attribute average_z_surface contains the derived surface averaged over the n_frames of the trajectory.

The attributes average_mean_curvature and average_gaussian_curvature contain the computed values of mean and Gaussian curvature averaged over the n_frames of the trajectory.

Example

You can pass a universe containing your selection of reference:

import MDAnalysis as mda
from membrane_curvature.base import MembraneCurvature

u = mda.Universe(coordinates, trajectory)
mc = MembraneCurvature(u).run()

surface =  mc.results.average_z_surface
mean_curvature =  mc.results.average_mean
gaussian_curvature = mc.results.average_gaussian

The respective 2D curvature plots can be obtained using the matplotlib package for data visualization via contourf() or imshow().

For specific examples visit the Usage page. Check the Visualization page for more examples to plot MembraneCurvature results using contourf() and imshow().