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
Parameters: *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
-
``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
-
delta
¶ MD integration timestep
-
n_atoms
¶ Number of atoms in a frame
-
n_frames
¶ Total number of frames in a trajectory
-
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.
-
``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
- 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, n_atoms=None, **kwargs)[source] 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
()[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.
-
``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
- 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
(n_atoms, **kwargs)[source] TRZ custom Timestep
Create a Timestep, representing a frame of a trajectory
Parameters: *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]
.