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1"""
2core.py
3MDAkit for Membrane Curvature
5Handles the primary functions
6"""
8from membrane_curvature.surface import normalized_grid, derive_surface, get_z_surface
9from membrane_curvature.curvature import mean_curvature, gaussian_curvature
10import time
11import MDAnalysis as mda
12import math
13from pathlib import Path
14__author__ = "Estefania Barreto-Ojeda"
15version = 0.1
18def main():
22 # 1. Populate universe with coordinates and trajectory
23 u = mda.Universe(topology, trajectory)
25 # 2 Set grid: Extract box dimension from MD sim,
26 # set grid max width, set number of unit cells
27 box_size = u.dimensions[0]
28 max_width = box_size * 0.1
29 n_cells = math.ceil(max_width / unit_width * 10)
31 # 3. Assign lipids in upper and lower leaflet
32 selection = u.select_atoms(atoms_upper, atoms_lower)
34 # 4. Save pickles zpo4
35 z_Ref = np.zeros([n_cells, n_cells])
36 z_coords = derive_surface(n_cells, selection, max_width)
38 # 5. Calculate curvature
39 K = gaussian_curvature(z_coords)
40 H = mean_curvature(z_coords)
42 return
45if __name__ == '__main__':
46 main()