mdciao.contacts.select_and_report_residue_neighborhood_idxs¶
-
mdciao.contacts.
select_and_report_residue_neighborhood_idxs
(ctc_freqs, res_idxs, fragments, residxs_pairs, top, ctcs_kept=5, restrict_to_resSeq=None, interactive=False, fraction=0.9, verbose=True)¶ Group residue pairs into neighborhoods using pre-computed contact frequencies
Returns a residue-index keyed dictionary containing the indices of
residxs_pairs
relevant for this residue.Can be used interactively to decide on-the-fly which residues to include in the neighborhood..
- Parameters
ctc_freqs (iterable of floats) – Contact frequencies between 0 and 1
res_idxs (list of integers) – list of residue idxs for which one wants to extract the neighborhoods
fragments (iterable of integers) – Fragments of the topology defined as list of non-overlapping residue indices
residxs_pairs (iterable of integer pairs) – The residue pairs for which the contact frequencies in
ctc_freqs
were computed.top (
Topology
) – The topology from which the residues comectcs_kept (integer or float, default is 5) –
Control how many contacts to report per residue. There’s two types of behaviour: * If int, it means directly keep these many contacts * if float, it must be in [0,1] and represents a fraction
of the total number of contacts to keep
restrict_to_resSeq (iterable, default is None) – Only cycle through the residues in
res_idxs
with these resSeq indices.interactive (boolean, default is False) – After reporting each neighborhood up to
ctcs_kept
, ask the user how many should be kept. Forces :obj:`verbose`=Truefraction (float, default is .9) – report how many contacts one needs to keep to arrive at this fraction of the overall contacts.
verbose (bool, default is True) – Be verbose
- Returns
selection – Dictionary keyed with residue indices and valued with lists of indices for
residxs_pairs
s.t. for example:selection[30] = [100,200]
means that for the residue with the index 300, the
residxs_pairs
on the 100-th and 200-th position, e.g. contain the pairs for its most frequent neighbors, e.g. [30-45] and [30-145].ctcs_kept
controls the length of the output, see also option ‘interactive’) Each i-th list is sorted by descending frequency of the contacts of residue-i and is truncated at freq==0 regardless ofctcs_kept
- Return type
dictionary