mdtraj.formats.NetCDFTrajectoryFile

class mdtraj.formats.NetCDFTrajectoryFile(filename, mode='r', force_overwrite=True)

Interface for reading and writing to AMBER NetCDF files. This is a file-like object, that supports both reading or 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’ and ‘w’ for ‘read’ and ‘write’, respectively.

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()	Close the NetCDF file handle
flush()	Write all buffered data in the to the disk file.
read([n_frames, stride, atom_indices])	Read data from a molecular dynamics trajectory in the AMBER NetCDF format.
read_as_traj(topology[, n_frames, stride, …])	Read a trajectory from a NetCDF file
seek(offset[, whence])	Move to a new file position
tell()	Current file position
write(coordinates[, time, cell_lengths, …])	Write one or more frames of a molecular dynamics trajectory to disk in the AMBER NetCDF format.

__init__(filename, mode='r', force_overwrite=True)

Methods

__init__(filename[, mode, force_overwrite])
close()	Close the NetCDF file handle
flush()	Write all buffered data in the to the disk file.
read([n_frames, stride, atom_indices])	Read data from a molecular dynamics trajectory in the AMBER NetCDF format.
read_as_traj(topology[, n_frames, stride, …])	Read a trajectory from a NetCDF file
seek(offset[, whence])	Move to a new file position
tell()	Current file position
write(coordinates[, time, cell_lengths, …])	Write one or more frames of a molecular dynamics trajectory to disk in the AMBER NetCDF format.

close()

Close the NetCDF file handle

flush()

Write all buffered data in the to the disk file.

read(n_frames=None, stride=None, atom_indices=None)

Read data from a molecular dynamics trajectory in the AMBER NetCDF format.

Parameters:

n_frames : int, optional

If n_frames is not None, the next n_frames of data from the file will be read. Otherwise, all of the frames in the file will be read.

stride : int, optional

If stride is not None, read only every stride-th frame from disk.

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=(n_frames, n_atoms, 3)

The cartesian coordinates of the atoms, in units of angstroms.

time : np.ndarray, None

The time corresponding to each frame, in units of picoseconds, or None if no time information is present in the trajectory.

cell_lengths : np.ndarray, None

The lengths (a,b,c) of the unit cell for each frame, 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.

read_as_traj(topology, n_frames=None, stride=None, atom_indices=None)

Read a trajectory from a NetCDF file

Parameters:

topology : Topology

The system topology

n_frames : int, optional

If positive, then read only the next n_frames frames. Otherwise read all of the frames in the file.

stride : np.ndarray, optional

Read only every stride-th frame.

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 containing the loaded portion of the file.

seek(offset, whence=0)

Move to a new file position

Parameters:

offset : int

A number of frames.

whence : {0, 1, 2}

0: offset from start of file, offset should be >=0. 1: move relative to the current position, positive or negative 2: move relative to the end of file, offset should be <= 0. Seeking beyond the end of a file is not supported

tell()

Current file position

Returns:

offset : int

The current frame in the file.

write(coordinates, time=None, cell_lengths=None, cell_angles=None)

Write one or more frames of a molecular dynamics trajectory to disk in the AMBER NetCDF format.

Parameters:

coordinates : np.ndarray, dtype=np.float32, shape=(n_frames, n_atoms, 3)

The cartesian coordinates of each atom, in units of angstroms.

time : np.ndarray, dtype=np.float32, shape=(n_frames), optional

The time index corresponding to each frame, in units of picoseconds.

cell_lengths : np.ndarray, dtype=np.double, shape=(n_frames, 3)

The lengths (a,b,c) of the unit cell for each frame.

cell_angles : np.ndarray, dtype=np.double, shape=(n_frames, 3)

The angles (lpha, eta, gamma) defining the unit cell for each frame.

Notes

If the input arrays are of dimension deficient by one, for example if the coordinates array is two dimensional, the time is a single scalar or cell_lengths and cell_angles are a 1d array of length three, that is okay. You’ll simply be saving a single frame.