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
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
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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;
None
selects the value ofMDAnalysis.core.flags
[‘convert_lengths’]. (see Flags)
-
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
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delta
MD integration timestep
-
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
-
numatoms
Number of atoms in a frame
-
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
-
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 ofMDAnalysis.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
Unit cell dimensions
[A,B,C,alpha,beta,gamma]
.
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