fast_forward.mapping module

fast_forward.mapping.create_new_universe(universe, mapped_trajectory, mappings, n_residues=None, res_iter=None)

Create a new universe according to the definitions in mappings the old universe, and the mapped trajectory.

:param universe fast_forward.universe_handler.UniverseHandler: :param mapped_trajectory: coordiante array with shape (n_frames, n_atoms, 3) :type mapped_trajectory: ndarray :param mappings: a dict of resname, mapping object Mapping :type mappings: dict

Returns:

the new universe that ties all information

Return type:

Universe

fast_forward.mapping.forward_map_indices(universe, mappings)

Map the universe atom indices to the new universe.

fast_forward.mapping.forward_map_positions(mapped_atoms, bead_idxs, weights, positions, n_frames, mode, treated_atoms)