mdciao.fragmentsΒΆ

Guess and manipulate fragments, i.e., sub-regions of molecular topologies. A fragment is just an iterable of integers representing the residue indices belonging to it.

Methods not documented here are either private or will be soon, please note the API is not yet stable.

get_fragments

Group residues of a molecular topology into fragments using different methods.

print_frag

Pretty-printing of fragments of an mtraj.topology

overview

Prints the fragments obtained by get_fragments for the available methods.

match_fragments

Align fragments of seq0 and seq1 pairwise and return a matrix of scores.

assign_fragments

Assign a parent fragment to each residue in a list of res_idxs