sponge.colvar.get_atoms

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sponge.colvar.get_atoms(atoms: Union[AtomsBase, List[AtomsBase], Tuple[AtomsBase], Tensor, Parameter, ndarray], batched: bool = False, keep_in_box: bool = False)[source]

get atom(s) or group.

Parameters

  • atoms (Union[list, tuple, AtomsBase, Tensor, Parameter, ndarray]) – List of atoms.

  • batched (bool) – Whether the first dimension of index is the batch size. Default: False.

  • keep_in_box (bool) – Whether to displace the coordinate in PBC box. Default: False.

Returns

atoms (Union[Atoms, Group]), Atoms or group.