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 (path-like) – 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

Attributes

distance_unit
topology	Get the topology out from the file