PlanarBase

class maicos.core.PlanarBase(atomgroup: AtomGroup, unwrap: bool, pack: bool, refgroup: AtomGroup | None, jitter: float, concfreq: int, dim: int, zmin: None | float, zmax: None | float, bin_width: float, wrap_compound: str)

Bases: AnalysisBase

Analysis class providing options and attributes for a planar system.

Parameters:

• atomgroup (MDAnalysis.core.groups.AtomGroup) – A AtomGroup for which the calculations are performed.

• dim ({0, 1, 2}) – Dimension for binning (x=0, y=1, z=1).

• zmin (float) – Minimal coordinate for evaluation (in Å) with respect to the center of mass of the refgroup. If zmin=None, all coordinates down to the lower cell boundary are taken into account.

• zmax (float) – Maximal coordinate for evaluation (in Å) with respect to the center of mass of the refgroup. If zmax = None, all coordinates up to the upper cell boundary are taken into account.

• bin_width (float) – Width of the bins (in Å).

• wrap_compound (str) – The group which will be kept together through the wrap processes. Allowed values are: "atoms", "group", "residues", "segments", "molecules", or "fragments".

results.bin_pos

Bin positions (in Å) ranging from zmin to zmax.

Type:

numpy.ndarray

zmin

Minimal coordinate for evaluation (Å) with in the lab frame, where 0 corresponds to the origin of the cell.

Type:

float

zmax

Maximal coordinate for evaluation (Å) with in the lab frame, where 0 corresponds to the origin of the cell.

Type:

float

_obs.L

Length (in Å) along the chosen dimension in the current frame.

Type:

float

_obs.bin_pos

Central bin positions (in Å) of each bin (in Å) in the current frame.

Type:

numpy.ndarray, (n_bins)

_obs.bin_width

Bin width (in Å) in the current frame

Type:

float

_obs.bin_edges

Edges of the bins (in Å) in the current frame.

Type:

numpy.ndarray, (n_bins + 1)

_obs.bin_area

Area of the rectangle of each bin in the current frame. Calculated via \(L_x \cdot L_y / N_\mathrm{bins}\) where \(L_x\) and \(L_y\) are the box lengths perpendicular to the dimension of evaluations given by dim. \(N_\mathrm{bins}\) is the number of bins.

Type:

numpy.ndarray, (n_bins)

_obs.bin_volume

Volume of an cuboid of each bin (in Å^3) in the current frame.

Type:

numpy.ndarray, (n_bins)

property odims: ndarray

Other dimensions perpendicular to dim i.e. (0,2) if dim = 1.