dupin.data.freud

Overview

FreudDescriptor

Provides an interface for using freud computes in dupin.

Details

Interface from freud to dupin.

freud is a Python package for analyzing molecular trajectory data.

The interface consist of a means of creating generators from freud computes. This implementation is not privledged and one could implement a generator from freud computes independent of this module.

Note

Requires the freud package.

class dupin.data.freud.FreudDescriptor(compute, attrs, compute_method='compute')

Provides an interface for using freud computes in dupin.

The generator produces a dictionary of compute attributes selected by the user. The feature identifiers (i.e. keys) are provided by the attrs constructor argument, and are the attribute names unless explicitly specified otherwise. See the constructor documentation for more information.

The generator wraps the compute method of the freud compute and takes the same signature for FreudDescriptor().

Parameters:

• compute – A freud object for computation.

• attrs (str or Sequence[str] or dict[str, str]) – If a string, the name of the attribute to use. This will also be the key name. If a sequence (list, tuple, etc) of string, all strings are considered attributes to use, and the string is used as the feature key as well. If a dictionary, the keys are the names of the attributes in the freud compute, and the values are the identifiers to use in dupin (None can be used as a proxy for the same as the attribute name). For two dimensional arrays, a list of strings is expected in place of a single string where each column is an independent feature.

• compute_method (str, optional) – The method name to use for computing the attrs specified. Defaults to “compute”.

Note

freud in some cases lumps multiple features into a two dimensional array where the rows are individual particles and columns are features. FreudDescriptor supports these features by using a list of string feature names in the constructor argument attrs.

__call__(*args, **kwargs)

Return computed attributes specified in a dictionary.

The keys of the dictionary are the attributes specified, unless a dict was passed for attrs, then then the keys are the values of that dict.

__init__(compute, attrs, compute_method='compute')