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

7.20.1. Classes

class MDAnalysis.coordinates.TRZ.Timestep(n_atoms, **kwargs)

TRZ custom Timestep

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.

frame

Index of current frame number (0 based)

time

Current system time in ps

n_atoms

Number of atoms in the frame (will be constant throughout trajectory)

pressure

System pressure in pascals

pressure_tensor

Array containing pressure tensors in order: xx, xy, yy, xz, yz, zz

total_energy

Hamiltonian for the system in kJ/mol

potential_energy

Potential energy of the system in kJ/mol

kinetic_energy

Kinetic energy of the system in kJ/mol

temperature

Temperature of the system in Kelvin

dimensions

Unit cell dimensions [A,B,C,alpha,beta,gamma].

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

Reads an IBIsCO or YASP trajectory file

ts

TRZ.Timestep – Timestep object containing coordinates of current frame

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).

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

Writer(filename, n_atoms=None)

A trajectory writer with the same properties as this trajectory.

close()

Close trz file if it was open

delta

MD integration timestep

n_atoms

Number of atoms in a frame

n_frames

Total number of frames in a trajectory

open_trajectory()

Open the trajectory file

skip_timestep

Timesteps between trajectory frames

class MDAnalysis.coordinates.TRZ.TRZWriter(filename, n_atoms, title='TRZ', convert_units=None)

Writes a TRZ format trajectory.

Note

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

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; None selects the value of MDAnalysis.core.flags [‘convert_lengths’]. (see Flags)

close()

Close if it was open

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

Reads an IBIsCO or YASP trajectory file

ts

TRZ.Timestep – Timestep object containing coordinates of current frame

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).

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

Writer(filename, n_atoms=None)

A trajectory writer with the same properties as this trajectory.

close()

Close trz file if it was open

delta

MD integration timestep

n_atoms

Number of atoms in a frame

n_frames

Total number of frames in a trajectory

open_trajectory()

Open the trajectory file

skip_timestep

Timesteps between trajectory frames

class MDAnalysis.coordinates.TRZ.TRZWriter(filename, n_atoms, title='TRZ', convert_units=None)

Writes a TRZ format trajectory.

Note

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

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; None selects the value of MDAnalysis.core.flags [‘convert_lengths’]. (see Flags)

close()

Close if it was open

class MDAnalysis.coordinates.TRZ.Timestep(n_atoms, **kwargs)

TRZ custom Timestep

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

Unit cell dimensions [A,B,C,alpha,beta,gamma].