mdtraj.formats.AmberNetCDFRestartFile¶
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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: filename : str
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_overwrite : bool, default=False
In write mode, if a file named filename already exists, clobber it and overwrite it
Attributes
n_atoms
n_frames
Methods
close
()flush
()read
([atom_indices])Read data from an AMBER NetCDF restart file read_as_traj
(topology[, atom_indices])Read an AMBER ASCII restart file as a trajectory. write
(coordinates[, time, cell_lengths, …])Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format. -
__init__
(filename, mode='r', force_overwrite=False)¶
Methods
__init__
(filename[, mode, force_overwrite])close
()flush
()read
([atom_indices])Read data from an AMBER NetCDF restart file read_as_traj
(topology[, atom_indices])Read an AMBER ASCII restart file as a trajectory. write
(coordinates[, time, cell_lengths, …])Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format. -
read
(atom_indices=None)¶ Read data from an AMBER NetCDF restart file
Parameters: atom_indices : np.ndarray, dtype=int, optional
The specific indices of the atoms you’d like to retrieve. If not supplied, all of the atoms will be retrieved.
Returns: coordinates : np.ndarray, shape=(1, n_atoms, 3)
The cartesian coordinates of the atoms, in units of angstroms. These files only ever contain 1 frame
time : np.ndarray, None
The time corresponding to the frame, in units of picoseconds, or None if no time information is present
cell_lengths : np.ndarray, None
The lengths (a, b, c) of the unit cell for the frame in angstroms, or None if the information is not present in the file
cell_angles : np.ndarray, None
The angles (lpha, eta, gamma) defining the unit cell for each frame, or None if the information is not present in the file.
Notes
If the file is not a NetCDF file with the appropriate convention, a TypeError is raised. If variables that are needed do not exist or if illegal values are passed in for parameters, ValueError is raised. If I/O errors occur, IOError is raised.
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read_as_traj
(topology, atom_indices=None)¶ Read an AMBER ASCII restart file as a trajectory.
Parameters: topology : Topology
The system topology
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.
Returns: trajectory : Trajectory
A trajectory object with 1 frame created from the file.
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write
(coordinates, time=None, cell_lengths=None, cell_angles=None)¶ Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format.
Parameters: coordinates : np.ndarray, dtype=np.float32, shape=([1,] n_atoms, 3)
The cartesian coordinates of each atom, in units of angstroms. Must be only a single frame (shape can be (1,N,3) or (N,3) where N is the number of atoms)
time : array-like with 1 element or float, optional
The time corresponding to this frame. If not specified, a place holder of 0 will be written
cell_lengths : np.ndarray, dtype=np.double, shape=([1,] 3)
The lengths (a,b,c) of the unit cell for the frame in Angstroms
cell_angles : np.ndarray, dtype=np.double, shape=([1,] 3)
The angles between the unit cell vectors for the frame in Degrees
Notes
You must only have one frame to write to this file.
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