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5.14. XYZ trajectory reader — MDAnalysis.coordinates.XYZ

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5.15. 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(arg, **kwargs)[source]

TRZ custom Timestep

frame

Index of current frame number (1 based)

time

Current system time in ps

numatoms

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[source]

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

class MDAnalysis.coordinates.TRZ.TRZReader(trzfilename, numatoms=None, convert_units=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

Creates a TRZ Reader

Arguments :
trzfilename

name of input file

numatoms

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[source]

MD integration timestep

dt[source]

The amount of time between frames in ps

Assumes that this step is constant (ie. 2 trajectories with different steps haven’t been stitched together) Returns 0 in case of IOError

numatoms[source]

Number of atoms in a frame

numframes[source]

Total number of frames in a trajectory

open_trajectory()[source]

Open the trajectory file

skip_timestep[source]

Timesteps between trajectory frames

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

Writes a TRZ format trajectory.

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

Create a TRZWriter

Arguments :
filename

name of output file

numatoms

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, numatoms=None, convert_units=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

Creates a TRZ Reader

Arguments :
trzfilename

name of input file

numatoms

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[source]

MD integration timestep

dt[source]

The amount of time between frames in ps

Assumes that this step is constant (ie. 2 trajectories with different steps haven’t been stitched together) Returns 0 in case of IOError

numatoms[source]

Number of atoms in a frame

numframes[source]

Total number of frames in a trajectory

open_trajectory()[source]

Open the trajectory file

skip_timestep[source]

Timesteps between trajectory frames

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

Writes a TRZ format trajectory.

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

Create a TRZWriter

Arguments :
filename

name of output file

numatoms

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(arg, **kwargs)[source]

TRZ custom Timestep

dimensions[source]

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