Utilities

atom_leaflet(;
    pdb_file,
    lipids)

Determines the leaflet of each atom of the lipid in a bilayer based on vertical position of the head atoms in the PDB structure file. Outputs an array of ±1s.

Keyword arguments

• pdb_file: PDB file;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;

atom_leaflet_dynamic(;
    coords,
    zs_m,
    Ls,
    pdb_file,
    lipids)

Dynamically determines the leaflet of each atom of the lipid in a bilayer based on vertical position of the head atoms in the trajectory coordinates. Outputs an array of ±1s.

Keyword arguments

• coords: a 3 × N array of N atoms coordinates;
• zs_m: bilayer midplane height;
• Ls: a tuple of the (Lx, Ly) dimensions of the box;
• pdb_file: PDB file;
• lipids: a list of lipids of type Lipid as defined in lipids.jl;

box_dimensions(;
    traj_file)

Calculates mean dimensions of the simulation box.

Keyword arguments

• traj_file: trajectory file;
• area_file: save area if not empty;
• box_dims_file: save simulation box dimensions if not empty;

blocking_error(a, n=10)

Calculates standard error of the mean for an array a divided in n blocks.

lipids_atoms_height(;
    pdb_file,
    traj_file,
    fs_file,
    output_dir,
    lipids)

Calculates the average distance of heavy atoms of each lipid from the midplane. Results for lipid "XXXX" will be saved to XXXX_zs.dat in output_dir.

Keyword arguments

• pdb_file: PDB structure file;
• traj_file: trajectory file;
• fs_file: fluctuation spectrum file;
• output_dir: output directory;
• lipids: a list of lipids of type Lipid as defined in lipids.jl.

peptide_atoms_height(;
    pdb_file,
    traj_file,
    output_file,
    lipids,
    n_residues)

Calculates average distance of CA atoms of each residue of peptide from the midplane.

Keyword arguments

• pdb_file: PDB structure file;
• traj_file: trajectory file;
• output_file: output file;
• lipids: a list of lipids of type Lipid as defined in lipids.jli;
• n_residues: number of residues in the peptide.

get_index_pairs(N)

Calculates all (n, m) index pairs and corresponding v = √(n^2 + m^2) values where v ≤ N.

find_ref_atoms(;
    input_dir,
    lipids,
    z,
    tolerance=2)

Determines the nearest atom to a determined height (such as the neutral surface) for each lipid and returns a dictionary.

Keyword arguments

• input_dir: directory with lipid atoms height files (e.g. XXXX_zs.dat for lipid "XXXX");
• lipids: a list of lipids of type Lipid as defined in lipids.jl;
• z: refrence surface height;
• tolerance: maximum distance from z accepted, will produce a warning if exceeded.

voronoi_shells(;
    points,
    box_dims,
    center,
    n_shells)

Determines the voronoi shells around a center point from a set of 2-D points (not including the center). Returns a dictionary with a list of point indices for each shell.

Keyword arguments

• points: a 2×N array of X and Y coordinates of the N points;
• box_dims: a tuple of simulation box lateral dimensions, Lx and Ly;
• cetner: coordinates of the center point;
• n_shells: number of voronoi shells to be determined.