mdtraj.compute_dssp

mdtraj.compute_dssp(traj, simplified=True)

Compute Dictionary of protein secondary structure (DSSP) secondary structure assignments

Parameters:

traj : md.Trajectory

A trajectory
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.

simplified : bool, default=True.

Use the simplified 3-category assignment scheme. Otherwise the original 8-category scheme is used.

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.

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

References

[R15]Kabsch W, Sander C (1983). “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features”. Biopolymers 22 (12): 2577-637. dio:10.1002/bip.360221211
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