Build Initial QI Phase Configurations

Classes

class bcc_build.BicontinuousCubicBuild(monomer, space_group, dimensions, weight_percent, density)

Bases: LLC_Membranes.llclib.topology.LC

__init__(monomer, space_group, dimensions, weight_percent, density)

Initialize a build of a bicontinuous cubic phase unit cell

Parameters:

• monomer (str) – name of monomer with which to build phase
• space_group (str) – name of space group into which monomers are arranged (i.e. gyroid, schwarzD etc.)
• dimensions (float, list of floats) – length of each edge of the unit cell (nm). The box is cubic, so they must all be the same (or just one length specified)
• weight_percent (int, float) – percent by weight of monomer in membrane
• density (float) – experimentally derived density of membrane

determine_monomer_placement(r=0.4)

Choose grid points where monomers will be placed

Parameters:r (float) – Any points within this distance of a chosen grid point will be removed as potential new grid points in an effort to keep point sufficiently spaced.

gen_grid(n, curvature, plot=False)

Create an n x n x n grid of points which lie close to the surface describing the unit cell space group

Parameters:

• n – number of points in the x, y and z direction
• curvature – determines mean curvature of hydrophilic/hydrophobic interface and thus whether the phase is

normal or inverted. {> 0 : QI phase, < 0: QII phase}’ :param plot: show a 3D scatter plot of the surface

place_monomers(shift=0)

Place monomers perpendicular to the space group surface at grid point locations

Parameters:shift (float) – translate monomer along vector perpendicular to space group surface by this amount (nm). This parameter effectively controls the pore size

reorder()

reorder coordinate, residues and atom names so that residues are separated