AlloViz.AlloViz.Filtering.Filtering#

class AlloViz.AlloViz.Filtering.Filtering(pkg, filtering, name, *, GetContacts_threshold=0, Sequence_Neighbor_distance=5, Interresidue_distance=10)[source]#

Bases: object

Class for network filtering

Instances of this class are used to be added as attributes to instances of Wrappers’ classes (as attributes of a AlloViz.Protein object) with the purpose of storing (un)filtered networks according to different criteria.

Raw network edges stored as a DataFrame in the passed pkg object are filtered with the corresponding function or combination of functions of the Filtering module and converted to individual NetworkX’ Graphs with _get_G() to be stored as private attributes.

Parameters:

pkginstance of a class from AlloViz.Wrappers: The object is used to retrieve the raw network edges for network analysis. It also contains/gives access to the corresponding:class:~AlloViz.Protein object and its information.
filteringstr or list: Filtering scheme(s) with which to filter the list of network edges. A list of strings is used to filter with a combination of criteria. All available (and combinable) filtering options are functions in the Filtering module: All(), GetContacts_edges(), No_Sequence_Neighbors(), GPCR_Interhelix(), Spatially_distant().
namestr: Name of the filtering scheme. It will be the same name as the passed filtering option if it is a single string, or the names of the filtering options joined by “_” if a lsit has been passed. It is used to name the pkg’s attribute in which the class instance is saved.

Other Parameters:

GetContacts_thresholdfloat: Optional kwarg that can be passed to specify the minimum contact frequency (0-1, default 0) threshold, which will be used to filter out contacts with a frequency (average) lower than it before analysis.
Sequence_Neighbor_distanceint: Optional kwarg that can be passed to specify the minimum number of sequence positions/distance between residues of a pair to retain in No_Sequence_Neighbors filtering, which defaults to 5.
Interresidue_distanceint or float: Optional kwarg that can be passed to specify the minimum number of angstroms that the CA atoms of residue pairs should have between each other in the initial PDB/structure (default 10 Å) to be considered spatially distant.