parmed.amber.NetCDFTraj¶
-
class
parmed.amber.NetCDFTraj(fname, mode='r')[source]¶ Class to read or write NetCDF restart files
- Parameters
- fnamestr
Name of the file to open
- modestr
- Mode to open in:
‘w’ means write-mode
‘r’ means read-mode
Notes
You should use the open_new and open_old alternative constructors instead of the default constructor
- Attributes
- box
- cell_lengths_angles
- coordinates
- forces
- remd_dimtype
- remd_indices
- temp0
- time
- velocities
Methods
add_box(lengths[, angles])Adds a new cell length and angle frame to the end of a NetCDF trajectory.
add_cell_lengths_angles(lengths[, angles])Adds a new cell length and angle frame to the end of a NetCDF trajectory.
add_coordinates(stuff)Adds a new coordinate frame to the end of a NetCDF trajectory.
add_forces(stuff)Adds a new coordinate frame to the end of a NetCDF trajectory.
add_remd_indices(stuff)Add REMD indices to the current frame of the NetCDF file
add_temp0(stuff)The temperature to add to the current frame of the NetCDF file
add_time(stuff)Adds the time to the current frame of the NetCDF file
add_velocities(stuff)Adds a new velocities frame to the end of a NetCDF trajectory.
close()Closes the NetCDF file
id_format(filename)Identifies the file type as an Amber NetCDF trajectory file
open_new(fname, natom, box[, crds, vels, …])Opens a new NetCDF file and sets the attributes
open_old(fname)Opens the NetCDF file and sets the global attributes that the file sets
flush
Methods
__init__(fname[, mode])Opens a NetCDF File
add_box(lengths[, angles])Adds a new cell length and angle frame to the end of a NetCDF trajectory.
add_cell_lengths_angles(lengths[, angles])Adds a new cell length and angle frame to the end of a NetCDF trajectory.
add_coordinates(stuff)Adds a new coordinate frame to the end of a NetCDF trajectory.
add_forces(stuff)Adds a new coordinate frame to the end of a NetCDF trajectory.
add_remd_indices(stuff)Add REMD indices to the current frame of the NetCDF file
add_temp0(stuff)The temperature to add to the current frame of the NetCDF file
add_time(stuff)Adds the time to the current frame of the NetCDF file
add_velocities(stuff)Adds a new velocities frame to the end of a NetCDF trajectory.
close()Closes the NetCDF file
flush()id_format(filename)Identifies the file type as an Amber NetCDF trajectory file
open_new(fname, natom, box[, crds, vels, …])Opens a new NetCDF file and sets the attributes
open_old(fname)Opens the NetCDF file and sets the global attributes that the file sets
Attributes