mdtraj.formats.LH5TrajectoryFile

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

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)[source]

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