mdtraj.formats.LH5TrajectoryFile

class mdtraj.formats.LH5TrajectoryFile(filename, mode='r', force_overwrite=True)

Interface for reading and writing to a MSMBuilder2 “LH5” molecular dynamics trajectory file, a deprecated format.

Parameters:

filename : str

Path to the file to open

mode : {‘r, ‘w’}

Mode in which to open the file. ‘r’ is for reading and ‘w’ is for writing

force_overwrite : bool

In mode=’w’, how do you want to behave if a file by the name of filename already exists? if force_overwrite=True, it will be overwritten.

Attributes

topology Get the topology out from the file

Methods

close() Close the HDF5 file handle
flush() Write all buffered data in the to the disk file.
read([n_frames, stride, atom_indices]) Read one or more frames of data from the file
read_as_traj([n_frames, stride, atom_indices]) Read a trajectory from the LH5 file
seek(offset[, whence]) Move to a new file position
tell() Current file position
write(coordinates) Write one or more frames of data to the file
__init__(filename, mode='r', force_overwrite=True)

Methods

__init__(filename[, mode, force_overwrite])
close() Close the HDF5 file handle
flush() Write all buffered data in the to the disk file.
read([n_frames, stride, atom_indices]) Read one or more frames of data from the file
read_as_traj([n_frames, stride, atom_indices]) Read a trajectory from the LH5 file
seek(offset[, whence]) Move to a new file position
tell() Current file position
write(coordinates) Write one or more frames of data to the file
close()

Close the HDF5 file handle

flush()

Write all buffered data in the to the disk file.

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

Read one or more frames of data from the file

Parameters:

n_frames : {int, None}

The number of frames to read. If not supplied, all of the remaining frames will be read.

stride : {int, None}

By default all of the frames will be read, but you can pass this flag to read a subset of of the data by grabbing only every stride-th frame from disk.

atom_indices : {int, None}

By default all of the atom will be read, but you can pass this flag to read only a subsets of the atoms for the coordinates and velocities fields. Note that you will have to carefully manage the indices and the offsets, since the i-th atom in the topology will not necessarily correspond to the i-th atom in your subset.
Returns:

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

The cartesian coordinates, in nanometers
read_as_traj(n_frames=None, stride=None, atom_indices=None)

Read a trajectory from the LH5 file

Parameters:

n_frames : {int, None}

The number of frames to read. If not supplied, all of the remaining frames will be read.

stride : {int, None}

By default all of the frames will be read, but you can pass this flag to read a subset of of the data by grabbing only every stride-th frame from disk.

atom_indices : {int, None}

By default all of the atom will be read, but you can pass this flag to read only a subsets of the atoms for the coordinates and velocities fields. Note that you will have to carefully manage the indices and the offsets, since the i-th atom in the topology will not necessarily correspond to the i-th atom in your subset.
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.
topology

Get the topology out from the file

Returns:

topology : mdtraj.Topology

A topology object
write(coordinates)

Write one or more frames of data to the file

Parameters:

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

The cartesian coordinates of the atoms in every frame, in nanometers.