SphereBase

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

Bases: AnalysisBase

Analysis class providing options and attributes for a spherical system.

Provide the results attribute r.

Parameters:

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

• 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_sph

positions in spherical coordinats (r, phi, theta)

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

Surface area (in Å^2) of the sphere of each bin with radius bin_pos in the current frame. Calculated via \(4 \pi r_i^2\) where \(i\) is the index of the bin.

Type:

numpy.ndarray, (n_bins)

results.bin_volume

volume of a spherical shell of each bins (in Å^3) of the current frame. Calculated via \(4\pi/3 \left(r_{i+1}^3 - r_i^3 \right)\) where i is the index of the bin.

Type:

numpy.ndarray, (n_bins)