Cylinder classes#

Base class for cylindrical analysis.

class maicos.core.cylinder.CylinderBase(atomgroups, rmin, rmax, **kwargs)[source]#

Bases: PlanarBase

Analysis class providing options and attributes for cylinder 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

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

  • 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.

  • jitter (float) –

    If jitter is not None, random numbers of the order of jitter (Å) are added to the atom positions.

    The appilication of a jitter is rationalized in possible aliasing effects when histogramming data, i.e., for spatial profiles. These aliasing effects can be stabilized with the application of a numerical jitter. The jitter value should be about the precision of the trajectory and will not alter the results of the histogram.

    You can estimate the precision of the positions in your trajectory with maicos.lib.util.trajectory_precision(). Note that if the precision is not the same for all frames, the smallest precision should be used.

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

  • 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.

  • kwargs (dict) – Parameters parsed to AnalysisBase.

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)

transform_positions(positions)[source]#

Transform positions into cylinder coordinates.

The origin of th coordinate system is at AnalysisBase.box_center. And the direction of the cylinder defined by self.dim.

Parameters:

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

Returns:

trans_positions – Positions in cylinder coordinates (r, phi, z)

Return type:

numpy.ndarray

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

Bases: CylinderBase, ProfileBase

Base class for computing radial profiles in a cylindrical 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

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

  • 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.

  • jitter (float) –

    If jitter is not None, random numbers of the order of jitter (Å) are added to the atom positions.

    The appilication of a jitter is rationalized in possible aliasing effects when histogramming data, i.e., for spatial profiles. These aliasing effects can be stabilized with the application of a numerical jitter. The jitter value should be about the precision of the trajectory and will not alter the results of the histogram.

    You can estimate the precision of the positions in your trajectory with maicos.lib.util.trajectory_precision(). Note that if the precision is not the same for all frames, the smallest precision should be used.

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

  • 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.

  • 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