dynsight.hdf5er.mda_to_hdf5

dynsight.hdf5er.mda_to_hdf5(mdatrajectory, targethdf5file, groupname, trajchunksize=100, override=False, attrs=None, trajslice=None, usetype='float64')[source]

Creates an HDF5 trajectory groupfrom an mda trajectory.

  • Original author: Daniele Rapetti

Opens or creates the given HDF5 file, request the user’s chosen group, then uploads an mda.Universe or an mda.AtomGroup to a h5py.Group in an hdf5 file

WARNING: in the HDF5 file if the chosen group is already present it will be overwritten by the new data

Parameters:

  • mdatrajectory (Universe | AtomGroup) – the container with the trajectory data

  • targethdf5file (str | pathlib.Path) – the name of HDF5 file

  • groupname (str) – the name of the group in wich save the trajectory data within the targetHDF5File

  • trajchunksize (int) – The desired dimension of the chunks of data that are stored in the hdf5 file. Defaults to 100.

  • override (bool) – If true the hdf5 file will be completely overwritten. Defaults to False.

  • attrs (dict | None) – Additional attributes.

  • trajslice (slice | None) – Slice of trajectory.

  • usetype (str) – The precision used to store the data. Defaults to “float64”.

Return type:

None