mdciao.contacts.GroupOfInterfaces

class mdciao.contacts.GroupOfInterfaces(dict_of_CGs, relabel_consensus=True)

Container for ContactGroup objects

Note

  • ATM the only ContactGroup s allowed are the ones that were initialized with some interface_residxs so that ContactGroup.is_interface will yield True

  • This object does not use residue indices at all and performs (and reports) all lookups with consensus labels The idea is that each contact group can have a different topologies. This is why relabel_consensus is True by default, because we cannot allow missing consensus labels beyond this point

__init__(dict_of_CGs, relabel_consensus=True)
Parameters

  • dict_of_CGs (dict) –

  • relabel_consensus (bool, default is True) –

Methods

__init__(dict_of_CGs[, relabel_consensus])

param dict_of_CGs

compare(**kwargs)

Very thin wrapper around mdciao.plots.compare_groups_of_contacts

interface_frequency_dict_by_consensus_labels(…)

Contact frequencies of the interface_matrix as a sparse dictionary of dicts double-keyed by consensus labels, e.g.

interface_matrix(ctc_cutoff_Ang)

Average of all interface_matrices contained in the this object

relabel_consensus(**kwargs)

Calls ContactGroup.relabel_consensus on all underlying contact groups

Attributes

conlab2matidx

Maps consensus labels (strings) to matrix indices of the interface_matrix

interface_labels_consensus

Union of all underlying consensus labels, split into the two interface members

interface_list

interface_names

The keys with which the object was initialized

interfaces

n_groups

compare(**kwargs)

Very thin wrapper around mdciao.plots.compare_groups_of_contacts

property conlab2matidx

Maps consensus labels (strings) to matrix indices of the interface_matrix

interface_frequency_dict_by_consensus_labels(ctc_cutoff_Ang, return_as_triplets=False)

Contact frequencies of the interface_matrix as a sparse dictionary of dicts double-keyed by consensus labels, e.g. res[key1][key2] : freq

Parameters

  • ctc_cutoff_Ang (float) –

  • return_as_triplets (bool) – instead of a dict [key1][key2]->freq res1-res2, return a list with triplets[[key1,key2,freq],…]

property interface_labels_consensus

Union of all underlying consensus labels, split into the two interface members

Note

The underlying ContactGroup.interface_labels_consensus is used

interface_matrix(ctc_cutoff_Ang)

Average of all interface_matrices contained in the this object

Parameters

ctc_cutoff_Ang (float) – The contact cutoff in Ang

Returns

mat – The rows contain the residues in interface_residxs`[0] and the columns the ones in :obj:`interface_residxs`[1]. Their consensus labels, in the same order, can be found in :obj:`interface_labels_consensus

Return type

ndarray

property interface_names

The keys with which the object was initialized

relabel_consensus(**kwargs)

Calls ContactGroup.relabel_consensus on all underlying contact groups

Parameters

kwargs (**) –