mdciao.fragments.fragment_slice

mdciao.fragments.fragment_slice(traj: mdtraj.Trajectory, fragments, keys_or_idxs=None)

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

Note

Regardless of the order in which the selection is done (e.g. keys_or_idxs=[1,0]) the returned sliced_traj will always be in ascending order atoms as they appear in traj

Parameters

• traj (mdtraj.Trajectory) – The trajectory to slice

• fragments (list or dict) – The fragment definitions as residue indices. Can be as a list or a as a dict, e.g. the output of mdciao.fragments.get_fragments (list) or mdciao.nomenclature.LabelerGPCR.top2frags (dict)

• keys_or_idxs (iterable or None) – The keys or indices of the fragments to slice to, i.e. to keep. If None, all all fragments are used as a selection

Returns

sliced_traj – A copy of traj only with the atoms present in the selected fragments

Return type

mdtraj.Trajectory