ProfileSphereBase

class maicos.core.ProfileSphereBase(atomgroup: AtomGroup, unwrap: bool, pack: bool, refgroup: AtomGroup | None, jitter: float, concfreq: int, rmin: float, rmax: None | float, bin_width: float, grouping: str, bin_method: str, output: str, weighting_function: Callable, weighting_function_kwargs: Dict | None, normalization: str)

Bases: SphereBase, ProfileBase

Base class for computing radial profiles in a spherical geometry.

For the correlation analysis the 0th bin of the 0th’s group profile is used. For further information on the correlation analysis please refer to AnalysisBase or the General design section.

Parameters:

• atomgroup (MDAnalysis.core.groups.AtomGroup) –

  A AtomGroup for which the calculations are performed. unwrap : bool When 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.

• pack (bool) –

  When True, molecules are put back into the unit cell. This is required because MAICoS only takes into account molecules that are inside the unit cell.

  If the input contains molecules that are already packed, speed up the calculation by disabling packing with pack=False.

• refgroup (MDAnalysis.core.groups.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 with respect to the center of the (changing) box.

• jitter (float) –

  Magnitude of the random noise to add to the atomic positions.

  A jitter can be used to stabilize the aliasing effects sometimes appearing when histogramming data. The jitter value should be about the precision of the trajectory. In that case, using jitter will not alter the results of the histogram. If jitter = 0.0 (default), the original atomic positions are kept unchanged.

  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.

• 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). grouping : {"atoms", "residues", "segments", "molecules", "fragments"} Atom grouping for the calculations.

  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 : {"com", "cog", "coc"} Method for the position binning.

  The possible options are center of mass ("com"), center of geometry ("cog"), and center of charge ("coc"). output : str Output filename.

• 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 weighting_function_kwargs. The function must return a numpy.ndarray with the same length as the number of group members.

• weighting_function_kwargs (dict) – Additional keyword arguments for weighting_function

• normalization ({"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.

results.bin_pos

Bin positions (in Å) ranging from rmin to rmax. results.profile : numpy.ndarray Calculated profile.

Type:

numpy.ndarray

results.dprofile

Estimated profile’s uncertainity.

Type:

numpy.ndarray