5.18. 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)[source]

TRZ custom Timestep

Create a Timestep, representing a frame of a trajectory

Arguments:
n_atoms

The total number of atoms this Timestep describes

Keywords:
positions

Whether this Timestep has position information [True]

velocities

Whether this Timestep has velocity information [False]

forces

Whether this Timestep has force information [False]

dt

The time difference between frames (ps). If time is set, then dt will be ignored.

time_offset

The starting time from which to calculate time (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)[source]

Reads an IBIsCO or YASP trajectory file

Data:
ts

Timestep object containing coordinates of current frame

Methods:
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

Arguments:
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()[source]

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()[source]

Open the trajectory file

skip_timestep

Timesteps between trajectory frames

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

Writes a TRZ format trajectory.

Methods:W = TRZWriter(trzfilename, n_atoms, title='TRZ')

Create a TRZWriter

Arguments:
filename

name of output file

n_atoms

number of atoms in trajectory

Keywords:
title

title of the trajectory

convert_units

units are converted to the MDAnalysis base format; None selects the value of MDAnalysis.core.flags [‘convert_lengths’]. (see Flags)

close()[source]

Close if it was open

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

Reads an IBIsCO or YASP trajectory file

Data:
ts

Timestep object containing coordinates of current frame

Methods:
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

Arguments:
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()[source]

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()[source]

Open the trajectory file

skip_timestep

Timesteps between trajectory frames

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

Writes a TRZ format trajectory.

Methods:W = TRZWriter(trzfilename, n_atoms, title='TRZ')

Create a TRZWriter

Arguments:
filename

name of output file

n_atoms

number of atoms in trajectory

Keywords:
title

title of the trajectory

convert_units

units are converted to the MDAnalysis base format; None selects the value of MDAnalysis.core.flags [‘convert_lengths’]. (see Flags)

close()[source]

Close if it was open

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

TRZ custom Timestep

Create a Timestep, representing a frame of a trajectory

Arguments:
n_atoms

The total number of atoms this Timestep describes

Keywords:
positions

Whether this Timestep has position information [True]

velocities

Whether this Timestep has velocity information [False]

forces

Whether this Timestep has force information [False]

dt

The time difference between frames (ps). If time is set, then dt will be ignored.

time_offset

The starting time from which to calculate time (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].