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

Classes to read IBIsCO / YASP binary trajectories.

Reads coordinates, velocities and more (see attributes of the Timestep).

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 (ps)
• versionchanged (.) – 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

Data:

ts

Timestep object containing coordinates of current frame

``len(trz)``

returns the number of frames

``for ts in trz``

iterates through the trajectory

``for ts in trz[start

stop:skip]`` iterate through a trajectory using slicing

``trz[i]``

random access of a trajectory frame

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* – name of input file
• *n_atoms* – number of atoms in trajectory, must taken from topology file!
• *convert_units* – converts units to MDAnalysis defaults

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.

``W = TRZWriter(trzfilename, n_atoms, title='TRZ')``

Create a TRZWriter

Parameters:

• *filename* – name of output file
• *n_atoms* – number of atoms in trajectory

Keywords:

title

title of the trajectory; the title must be 80 characters or shorter, a longer title raises a ValueError exception.

convert_units

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

Data:

ts

Timestep object containing coordinates of current frame

``len(trz)``

returns the number of frames

``for ts in trz``

iterates through the trajectory

``for ts in trz[start

stop:skip]`` iterate through a trajectory using slicing

``trz[i]``

random access of a trajectory frame

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* – name of input file
• *n_atoms* – number of atoms in trajectory, must taken from topology file!
• *convert_units* – converts units to MDAnalysis defaults

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.

``W = TRZWriter(trzfilename, n_atoms, title='TRZ')``

Create a TRZWriter

Parameters:

• *filename* – name of output file
• *n_atoms* – number of atoms in trajectory

Keywords:

title

title of the trajectory; the title must be 80 characters or shorter, a longer title raises a ValueError exception.

convert_units

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 (ps)
• versionchanged (.) – 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].