Sphere classes#

Base class for spherical analysis.

class maicos.core.sphere.ProfileSphereBase(weighting_function, normalization, atomgroups, grouping, bin_method, output, f_kwargs=None, **kwargs)[source]#

Bases: SphereBase, ProfileBase

Base class for computing radial profiles in a spherical geometry.

Parameters:

  • weighting_function (callable) – The function calculating the array weights for the histogram analysis. It must take an Atomgroup as first argument and a grouping (‘atoms’, ‘residues’, ‘segments’, ‘molecules’, ‘fragments’) as second. Additional parameters can be given as f_kwargs. The function must return a numpy.ndarray with the same length as the number of group members.

  • normalization (str {'None', 'number', 'volume'}) – The normalization of the profile performed in every frame. If None no normalization is performed. If number the histogram is divided by the number of occurences in each bin. If volume the profile is divided by the volume of each bin.

  • f_kwargs (dict) – Additional parameters for function

  • atomgroups (list[AtomGroup]) – a list of AtomGroup objects for which the calculations are performed.

  • refgroup (AtomGroup) –

    Reference AtomGroup used for the calculation.

    If refgroup is provided, the calculation is performed relative to the center of mass of the AtomGroup.

    If refgroup is None the calculations are performed to the center of the (changing) box.

  • unwrap (bool) –

    When unwrap = True, molecules that are broken due to the periodic boundary conditions are made whole.

    If the input contains molecules that are already whole, speed up the calculation by disabling unwrap. To do so, use the flag -no-unwrap when using MAICoS from the command line, or use unwrap = False when using MAICoS from the Python interpreter.

    Note: Molecules containing virtual sites (e.g. TIP4P water models) are not currently supported in MDAnalysis. In this case, you need to provide unwrapped trajectory files directly, and disable unwrap. Trajectories can be unwrapped, for example, using the trjconv command of GROMACS.

  • concfreq (int) – When concfreq (for conclude frequency) is larger than 0, the conclude function is called and the output files are written every concfreq frames

  • 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).

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

  • rmax –

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

    If rmax=None, the box extension is taken.

  • grouping (str {'atoms', 'residues', 'segments', 'molecules', 'fragments'}) –

    Atom grouping for the calculations of profiles.

    The possible grouping options are the atom positions (in the case where grouping='atoms') or the center of mass of the specified grouping unit (in the case where grouping='residues', 'segments', 'molecules' or 'fragments').

  • bin_method (str {'cog', 'com', 'coc'}) –

    Method for the position binning.

    The possible options are center of geometry (cog), center of mass (com), and center of charge (coc).

  • output (str) – Output filename.

results.bin_pos#

Bin positions (in Å) ranging from rmin to rmax.

Type:

numpy.ndarray

results.profile#

Calculated profile.

Type:

numpy.ndarray

results.dprofile#

Estimated profile’s uncertainity.

Type:

numpy.ndarray

class maicos.core.sphere.SphereBase(atomgroups, rmin, rmax, bin_width, **kwargs)[source]#

Bases: AnalysisBase

Analysis class providing options and attributes for spherical system.

Provide the results attribute r.

Parameters:

  • atomgroups (Atomgroup or list[Atomgroup]) – Atomgroups taken for the Analysis

  • refgroup (AtomGroup) –

    Reference AtomGroup used for the calculation.

    If refgroup is provided, the calculation is performed relative to the center of mass of the AtomGroup.

    If refgroup is None the calculations are performed to the center of the (changing) box.

  • unwrap (bool) –

    When unwrap = True, molecules that are broken due to the periodic boundary conditions are made whole.

    If the input contains molecules that are already whole, speed up the calculation by disabling unwrap. To do so, use the flag -no-unwrap when using MAICoS from the command line, or use unwrap = False when using MAICoS from the Python interpreter.

    Note: Molecules containing virtual sites (e.g. TIP4P water models) are not currently supported in MDAnalysis. In this case, you need to provide unwrapped trajectory files directly, and disable unwrap. Trajectories can be unwrapped, for example, using the trjconv command of GROMACS.

  • concfreq (int) – When concfreq (for conclude frequency) is larger than 0, the conclude function is called and the output files are written every concfreq frames

  • 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).

  • kwargs (dict) – Parameters parsed to AnalysisBase.

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 \(\left 4\pi/3(r_{i+1}^3 - r_i^3 \right)\) where i is the index of the bin.

Type:

numpy.ndarray, (n_bins)

transform_positions(positions)[source]#

Transform positions into spherical coordinates.

The origin of th coordinate system is at AnalysisBase.box_center.

Parameters:

positions (numpy.ndarray) – Cartesian coordinates (x,y,z)

Returns:

trans_positions – Positions in spherical coordinates (r, phi, theta)

Return type:

numpy.ndarray