6.5. DESRES file format — MDAnalysis.coordinates.DMS

Classes to read DESRES Molecular Structure file format (DMS) coordinate files (as used by the Desmond MD package).

class MDAnalysis.coordinates.DMS.DMSReader(filename, convert_units=None, n_atoms=None, **kwargs)[source]

Reads both coordinates and velocities.

Changed in version 0.11.0: Frames now 0-based instead of 1-based

class MDAnalysis.coordinates.DMS.Timestep(n_atoms, **kwargs)[source]

Create a Timestep, representing a frame of a trajectory

Parameters:
  • n_atoms (int) – The total number of atoms this Timestep describes
  • positions (bool, optional) – Whether this Timestep has position information [True]
  • velocities (bool (optional)) – Whether this Timestep has velocity information [False]
  • forces (bool (optional)) – Whether this Timestep has force information [False]
  • reader (Reader (optional)) – A weak reference to the owning Reader. Used for when attributes require trajectory manipulation (e.g. dt)
  • dt (float (optional)) – The time difference between frames (ps). If time is set, then dt will be ignored.
  • time_offset (float (optional)) – The starting time from which to calculate time (in ps)

Changed in version 0.11.0: Added keywords for positions, velocities and forces. Can add and remove position/velocity/force information by using the has_* attribute.

dimensions

unitcell dimensions (A, B, C, alpha, beta, gamma)