mdciao.fragments

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.
fragment_slice	Slice a geometry using arbitrary fragment definitions, a la mdtraj.Trajectory.atom_slice
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