mdciao.nomenclature.guess_nomenclature_fragments

mdciao.nomenclature.guess_nomenclature_fragments(refseq, top, fragments=None, min_hit_rate=0.6, verbose=False, return_residue_idxs=False, empty=<class 'list'>)

Guess what fragments in the topology best match the consensus labels in a LabelerConsensus object

The guess uses a cutoff, min_hit_rate, for the quality of each segment’s alignment to the sequence in CLin.

It only counts the matches for the protein residues of top, i.e. waters, ions, non-peptidic polymers are note taken into account.

You can use the method to identify the receptor in topology where other molecules (e.g. the Gprot) are present (or the other way around)

Parameters

  • refseq (str or LabelerConsensus) – If not str, the sequence will be gotten from LabelerConsensus.seq method

  • top – Topology object or string containing the sequence.

  • fragments (iterable of iterables of idxs) – How top is split into fragments If None, will be generated using get_fragments defaults

  • min_hit_rate (float, default is .6) – Only fragments with hit rates higher than this will be returned as a guess

  • verbose (boolean) – be verbose

  • return_residue_idxs (bool, default is False) – Return the list residue indices directly, instead of returning a list of fragment idxs.

  • empty (class, list or None, default is list) – What to return in case of an emtpy guess, an empty list or a None

Returns

guess – indices of the fragments (or residues) with higher hit-rate than min_hit_rate

Return type

list