mdtraj.formats.AmberNetCDFRestartFile¶
-
class
mdtraj.formats.
AmberNetCDFRestartFile
(filename, mode='r', force_overwrite=False)¶ Interface for reading and writing AMBER NetCDF files. This is a file-like object, that supports both reading and writing depending on the mode flag. It implements the context manager protocol, so you can also use it with the python ‘with’ statement.
- Parameters
- filenamestr
The name of the file to open
- mode{‘r’, ‘w’}, default=’r’
The mode in which to open the file. Valid options are ‘r’ or ‘w’ for ‘read’ or ‘write’
- force_overwritebool, default=False
In write mode, if a file named filename already exists, clobber it and overwrite it
- Attributes
- n_atoms
- n_frames
Methods
read
(self[, atom_indices])Read data from an AMBER NetCDF restart file
read_as_traj
(self, topology[, atom_indices])Read an AMBER ASCII restart file as a trajectory.
write
(self, coordinates[, time, …])Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format.
close
flush
-
__init__
(self, filename, mode='r', force_overwrite=False)¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__
(self, filename[, mode, force_overwrite])Initialize self.
close
(self)flush
(self)read
(self[, atom_indices])Read data from an AMBER NetCDF restart file
read_as_traj
(self, topology[, atom_indices])Read an AMBER ASCII restart file as a trajectory.
write
(self, coordinates[, time, …])Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format.
Attributes
distance_unit
n_atoms
n_frames