AlloViz.AlloViz.Filtering.GetContacts_edges#

AlloViz.AlloViz.Filtering.GetContacts_edges(pkg, data, GetContacts_threshold, **kwargs)[source]#

Retain only edges found by GetContacts

It retains only the raw edges for which GetContacts has been able to calculate a contact frequency value, i.e., residue pairs that are in physicochemical contact.

GetContacts data is retrieved from the passed pkg’s Protein object stored in it and thus is needed to have been calculated previously. It may (or not) have been calculated using the GetContacts_threshold kwarg, filtered afterwards with AlloViz.Wrappers.GetContacts.GetContacts.filter_contacts(), or the GetContacts_threshold kwarg can also be passed to the analysis to filter the GetContacts data in this point.

Other Parameters:

**kwargs: GetContacts_threshold kwarg 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.