CylinderBase

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

Bases: PlanarBase

Analysis class providing options and attributes for a cylinder system.

Provide the results attribute r.

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.

• rmin (float) – Minimal radial coordinate relative to the center of mass of the refgroup for evaluation (in Å).

• rmax (float) –

  Maximal radial coordinate relative to the center of mass of the refgroup for evaluation (in Å).

  If rmax=None, the box extension is taken.

• 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 rmin to rmax.

Type:

numpy.ndarray

pos_cyl

positions in cylinder coordinats (r, phi, z)

Type:

numpy.ndarray

_obs.R

Average length (in Å) along the radial dimension in the current frame.

Type:

float

_obs.bin_pos

Central bin position 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 annulus pf the each bin in the current frame. Calculated via \(\pi \left( r_{i+1}^2 - r_i^2 \right)\) where i is the index of the bin.

Type:

numpy.ndarray, (n_bins)

_obs.bin_volume

Volume of an hollow cylinder of each bin (in Å^3) in the current frame. Calculated via \(\pi L \left( r_{i+1}^2 - r_i^2 \right)\) where i is the index of the bin.

Type:

numpy.ndarray, (n_bins)