AlloViz.Protein.filter¶
- Protein.filter(pkgs='all', filterings='All', *, GetContacts_threshold=0, Sequence_Neighbor_distance=5, Interresidue_distance=10)[source]¶
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 theAlloViz.AlloViz.Filtering.Filtering
class. The different filtering options are detailed in theFiltering
module.- Parameters:
- pkgsstr or list, default: “all”
Package(s)/Network construction method(s) for which to analyze their raw edge weights, which must be already calculated and their data saved as instance attribute. In this case, “all” sends the computation for all available methodsthat are already calculated and saved as instance attributes.
- 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” (capitalized) performs NONE of the available filtering schemes. “all” (lowercase!) 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.filter("dynetan", ["GetContacts_edges", ["GetContacts_edges", "GPCR_Interhelix"]]) >>> opioidGPCR.dynetan.GetContacts_edges_GPCR_Interhelix <AlloViz.AlloViz.Filtering.Filtering at 0x7f892c3c0fa0>