# Source code for mdtraj.geometry.dssp

    import numpy as np

    from mdtraj.geometry import _geometry
    from mdtraj.geometry.hbond import _prep_kabsch_sander_arrays

    SIMPLIFIED_CODE_TRANSLATION = str.maketrans("HGIEBTS ", "HHHEECCC")

    __all__ = ["compute_dssp"]

    def compute_dssp(traj, simplified=True):
        """Compute Dictionary of protein secondary structure (DSSP) secondary structure assignments

        Parameters
        ----------
        traj : md.Trajectory
            A trajectory
        simplified : bool, default=True
            Use the simplified 3-category assignment scheme. Otherwise the original
            8-category scheme is used.

        Returns
        -------
        assignments : np.ndarray, shape=(n_frames, n_residues), dtype=S1
            The assignments is a 2D array of character codes (see below), giving
            the secondary structure of each residue in each frame.

        Notes
        -----
        The DSSP assignment codes are:

           - 'H' : Alpha helix
           - 'B' : Residue in isolated beta-bridge
           - 'E' : Extended strand, participates in beta ladder
           - 'G' : 3-helix (3/10 helix)
           - 'I' : 5 helix (pi helix)
           - 'T' : hydrogen bonded turn
           - 'S' : bend
           - ' ' : Loops and irregular elements

        The simplified DSSP codes are:

           - 'H' : Helix. Either of the 'H', 'G', or 'I' codes.
           - 'E' : Strand. Either of the 'E', or 'B' codes.
           - 'C' : Coil. Either of the 'T', 'S' or ' ' codes.

        A special 'NA' code will be assigned to each 'residue' in the topology which
        isn't actually a protein residue (does not contain atoms with the names
        'CA', 'N', 'C', 'O'), such as water molecules that are listed as 'residue's
        in the topology.

        Our implementation is based on DSSP-2.2.0, written by Maarten L. Hekkelman
        and distributed under the Boost Software license.

        References
        ----------
        .. [1] Kabsch W, Sander C (1983). "Dictionary of protein secondary
           structure: pattern recognition of hydrogen-bonded and geometrical
           features". Biopolymers 22 (12): 2577-637. doi:10.1002/bip.360221211
        """
        if traj.topology is None:
            raise ValueError("kabsch_sander requires topology")

        (
            xyz,
            nco_indices,
            ca_indices,
            proline_indices,
            protein_indices,
        ) = _prep_kabsch_sander_arrays(traj)
        chain_ids = np.array([r.chain.index for r in traj.top.residues], dtype=np.int32)

        value = _geometry._dssp(xyz, nco_indices, ca_indices, proline_indices, chain_ids)
        if simplified:
            value = value.translate(SIMPLIFIED_CODE_TRANSLATION)

        n_frames = xyz.shape[0]
        n_residues = nco_indices.shape[0]

        array = np.fromiter(value, dtype=np.dtype("U2"))

        array = array.reshape(n_frames, n_residues)
        array[:, np.logical_not(protein_indices)] = "NA"
        return array