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).
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class
MDAnalysis.coordinates.TRZ.Timestep(arg, **kwargs)[source]¶ TRZ custom Timestep
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frame¶ Index of current frame number (1 based)
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time¶ Current system time in ps
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numatoms¶ Number of atoms in the frame (will be constant throughout trajectory)
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pressure¶ System pressure in pascals
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pressure_tensor¶ Array containing pressure tensors in order: xx, xy, yy, xz, yz, zz
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total_energy¶ Hamiltonian for the system in kJ/mol
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potential_energy¶ Potential energy of the system in kJ/mol
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kinetic_energy¶ Kinetic energy of the system in kJ/mol
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temperature¶ Temperature of the system in Kelvin
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dimensions¶ Unit cell dimensions
[A,B,C,alpha,beta,gamma].
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class
MDAnalysis.coordinates.TRZ.TRZReader(trzfilename, numatoms=None, convert_units=None, **kwargs)[source]¶ Reads an IBIsCO or YASP trajectory file
Data: - ts
Timestepobject containing coordinates of current frame
Methods: len(trz)returns the number of frames
for ts in trziterates 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
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delta¶ MD integration timestep
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dt¶ 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
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numatoms¶ Number of atoms in a frame
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numframes¶ Total number of frames in a trajectory
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skip_timestep¶ Timesteps between trajectory frames
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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;
Noneselects the value ofMDAnalysis.core.flags[‘convert_lengths’]. (see Flags)
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class
MDAnalysis.coordinates.TRZ.TRZReader(trzfilename, numatoms=None, convert_units=None, **kwargs)[source] Reads an IBIsCO or YASP trajectory file
Data: - ts
Timestepobject containing coordinates of current frame
Methods: len(trz)returns the number of frames
for ts in trziterates 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
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close()[source] Close trz file if it was open
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delta MD integration timestep
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dt 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
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numatoms Number of atoms in a frame
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numframes Total number of frames in a trajectory
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open_trajectory()[source] Open the trajectory file
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skip_timestep Timesteps between trajectory frames
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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;
Noneselects the value ofMDAnalysis.core.flags[‘convert_lengths’]. (see Flags)
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close()[source] Close if it was open
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class
MDAnalysis.coordinates.TRZ.Timestep(arg, **kwargs)[source] TRZ custom Timestep
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dimensions Unit cell dimensions
[A,B,C,alpha,beta,gamma].
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