openfe_analysis.reader

Classes

FEReader(*args, **kwargs)

MDAnalysis Reader for NetCDF files created by openmmtools.multistate.MultiStateReporter
class openfe_analysis.reader.FEReader(*args: Any, **kwargs: Any)

MDAnalysis Reader for NetCDF files created by openmmtools.multistate.MultiStateReporter

Provides a 1D trajectory along either:

  • constant Hamiltonian state (index_method=”state”)

  • constant replica (index_method=”replica”)

selected via the index argument.

Parameters:

  • filename (pathlike or nc.Dataset) – Path to the .nc file or an open Dataset.

  • 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.

  • convert_units (bool) – Convert positions to Angstrom.

format = 'MultiStateReporter'
units = {'length': 'nanometer', 'time': 'ps'}
property multistate_index: int
property n_atoms: int
property n_frames: int
property index_method: str
static parse_n_atoms(filename, **kwargs) → int

Determine the number of atoms stored in a MultiStateReporter NetCDF file.

Parameters:

filename (path-like) – Path to the NetCDF file.

Returns:

Number of atoms in the system.

Return type:

int

property dt: float
close()