Reader

HAS_MDANALYSIS = True

MDAnalysisReader

Bases: Reader

Read data via MDAnalysis.

checks()

extract(prj, ens_id, run_id, ctx)

Extract and parse all possible information given the context. This method is responsible for calling all other methods.

parse_atom_z(prj, ens_id, ctx, run_id=None)

Store the atomic numbers as an ensemble-level array.

parse_coordinates(prj, ens_id, ctx, run_id=None)

Stack all frames into a (n_frames, n_atoms, 3) array.

parse_ensemble_metadata(prj, ens_id, ctx, run_id=None)

Store per-ensemble atom symbols & ff types once.

parse_topology(prj, ens_id, ctx, run_id=None)

Store topology.

prepare(topology, trajectory, *args, **kwargs)

Load a single Universe.