6.22. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ

Classes to read IBIsCO / YASP TRZ binary trajectories, including coordinates, velocities and more (see attributes of the Timestep).

Data are read and written in binary representation but because this depends on the machine hardware architecture, MDAnalysis always reads and writes TRZ trajectories in little-endian byte order.

6.22.1. Classes

class MDAnalysis.coordinates.TRZ.TRZReader(trzfilename, n_atoms=None, **kwargs)

Reads an IBIsCO or YASP trajectory file

ts

Timestep object containing coordinates of current frame

Type:

timestep.Timestep

Note

Binary TRZ trajectories are always assumed to be written in little-endian byte order and are read as such.

Changed in version 0.11.0: Frames now 0-based instead of 1-based. Extra data (Temperature, Energies, Pressures, etc) now read into ts.data dictionary. Now passes a weakref of self to ts (ts._reader).

Changed in version 1.0.1: Now checks for the correct n_atoms on reading and can raise ValueError.

Changed in version 2.1.0: TRZReader now returns a default dt of 1.0 when it cannot be obtained from the difference between two frames.

Changed in version 2.3.0: _frame attribute moved to ts.data dictionary.

Deprecated since version 2.7.0: The TRZ Reader and Writer are deprecated as of version 2.7.0 and will be removed in version 3.0.0.

Creates a TRZ Reader

Parameters:

• trzfilename (str) – name of input file

• n_atoms (int) – number of atoms in trajectory, must be taken from topology file!

• convert_units (bool (optional)) – converts units to MDAnalysis defaults

Raises:

ValueError – If n_atoms or the number of atoms in the topology file do not match the number of atoms in the trajectory.

Writer(filename, n_atoms=None)

A trajectory writer with the same properties as this trajectory.

close()

Close trz file if it was open

property delta

MD integration timestep

property n_atoms

Number of atoms in a frame

property n_frames

Total number of frames in a trajectory

open_trajectory()

Open the trajectory file

property skip_timestep

Timesteps between trajectory frames

units = {'length': 'nm', 'time': 'ps', 'velocity': 'nm/ps'}

dict with units of of time and length (and velocity, force, … for formats that support it)

class MDAnalysis.coordinates.TRZ.TRZWriter(filename, n_atoms, title='TRZ', convert_units=True)

Writes a TRZ format trajectory.

Note

Binary TRZ trajectories are always written in little-endian byte order.

Deprecated since version 2.7.0: The TRZ Reader and Writer are deprecated as of version 2.7.0 and will be removed in version 3.0.0.

Create a TRZWriter

Parameters:

• filename (str) – name of output file

• n_atoms (int) – number of atoms in trajectory

• title (str (optional)) – title of the trajectory; the title must be 80 characters or shorter, a longer title raises a ValueError exception.

• convert_units (bool (optional)) – units are converted to the MDAnalysis base format; [True]

close()

Close if it was open

units = {'length': 'nm', 'time': 'ps', 'velocity': 'nm/ps'}

dict with units of of time and length (and velocity, force, … for formats that support it)