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.
- pkginstance of a class from
- 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.
See also
AlloViz.Protein.filter
Class method to filter the network(s) raw edge weights with different criteria.
AlloViz.Wrappers.Base.Base.filter
Pkg’s method to filter the network(s) raw edge weights with different criteria.
- Attributes:
- graphsdict of external:ref:Graph <graph> objects
Methods
analyze
([elements, metrics, cores, ...])Analyze the filtered network