md.data.HDF5Loader

class md.data.HDF5Loader(hdf5_database: str, skip_initial: int | None = 0, load_properties: bool | None = True)[source]

Class for loading HDF5 datasets written by the FileLogger. By default, this requires at least a MoleculeStream to be present. PropertyData is also read by default, but can be disabled.

Parameters:

hdf5_database (str) – Path to the database file.
skip_initial (int) – Skip the initial N configurations in the trajectory, e.g. to account for equilibration (default=0).
load_properties (bool) – Extract and reconstruct the property data stored by a PropertyStream (e.g. forces, energies, etc.), enabled by default.