AlloViz.Wrappers.CARDS_w.CARDS_Disorder_mediated_Backbone_Dihs.filter

CARDS_Disorder_mediated_Backbone_Dihs.filter(filterings='All', **kwargs)

Filter network edges

Filter the networks according to the selected criteria to perform analyses on (all or) a subset of the edges. It calls AlloViz.Wrappers.Base.Base.filter() and results are stored in instances of the AlloViz.AlloViz.Filtering.Filtering class. The different filtering options are detailed in the Filtering module.

Parameters:

filteringsstr or list of strs and/or lists, default: “all”

Filtering scheme(s) with which to filter the list of network edges before analysis. It can be a string, or a list of strings and/or lists: a list of lists (also with or without 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(). The default “all” performs all the available filtering schemes (no combinations).

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.AlloViz.Filtering.Filtering

Filtering class.

AlloViz.Protein.calculate

Class method to calculate the network(s) raw edge weights with different network construction methods.

AlloViz.Protein.analyze

Class method to analyze the calculated raw edge weights with graph theory-based methods.

AlloViz.Protein.view

Class method to visualize the network on the protein structure.

Examples

>>> opioidGPCR = AlloViz.Protein(GPCR=169)
>>> opioidGPCR.calculate(["getcontacts", "dynetan"], cores=6, taskcpus=2)
>>> opioidGPCR.dynetan.filter(["GetContacts_edges", ["GetContacts_edges", "GPCR_Interhelix"]])
>>> opioidGPCR.dynetan.GetContacts_edges_GPCR_Interhelix
<AlloViz.AlloViz.Filtering.Filtering at 0x7f892c3c0fa0>