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.

__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

Attributes

distance_unit
topology	Get the topology out from 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.