openfe_analysis.utils.multistate

Functions

trajectory_from_multistate(input_file, ...)

Extract a 1D trajectory (in an AMBER compliant format) from a MultiState sampler generated NetCDF file.
openfe_analysis.utils.multistate.trajectory_from_multistate(input_file: Path, output_file: Path, index: int, index_method: Literal['state', 'replica'] = 'state') → None

Extract a 1D trajectory (in an AMBER compliant format) from a MultiState sampler generated NetCDF file.

Parameters:

  • input_file (path.Pathlib) – Path to the input MultiState sampler generated NetCDF file.

  • output_file (path.Pathlib) – Path to the AMBER-style NetCDF trajectory to be written.

  • index (int) – Index of the state or replica to extract. May be negative.

  • index_method ({"state", "replica"}, default "state") – Whether index refers to a Hamiltonian state or a replica.