ProfileBase

class maicos.core.ProfileBase(atomgroup: AtomGroup, grouping: str, bin_method: str, output: str, weighting_function: Callable, weighting_function_kwargs: None | Dict, normalization: str)

Bases: object

Base class for computing profiles.

Parameters:

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

• 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.profile

Calculated profile.

Type:

numpy.ndarray

results.dprofile

Estimated profile’s uncertainity.

Type:

numpy.ndarray

save() → None

Save results of analysis to file specified by output.