openfe_analysis.utils.plotting

Functions

plot_2D_rmsd(data[, vmax])

Plots 2D RMSD for many states

plot_ligand_COM_drift(time, data)

Plot ligand center-of-mass drift over time for each thermodynamic state.

plot_ligand_RMSD(time, data)

Plot ligand RMSD over time for each thermodynamic state.
openfe_analysis.utils.plotting.plot_2D_rmsd(data: list[ndarray] | list[list[float]], vmax: float = 5.0) → Figure

Plots 2D RMSD for many states

Parameters:

  • data (list[np.ndarray] | list[list[float]]) – for each state, the 2D RMSD

  • vmax (float, optional) – the value to consider “high” in the colourmap to flag bad values, defaults to 5.0 (A)

Return type:

matplotlib Figure

openfe_analysis.utils.plotting.plot_ligand_COM_drift(time: list[float], data: list[ndarray]) → Figure

Plot ligand center-of-mass drift over time for each thermodynamic state.

Parameters:

  • time (list[float]) – Time values in picoseconds.

  • data (list[np.ndarray]) – Per-state ligand COM drift.

Return type:

matplotlib.figure.Figure

openfe_analysis.utils.plotting.plot_ligand_RMSD(time: list[float], data: list[ndarray]) → Figure

Plot ligand RMSD over time for each thermodynamic state.

Parameters:

  • time (list[float]) – Time values in picoseconds.

  • data (list[np.ndarray]) – Per-state ligand RMSD.

Return type:

matplotlib.figure.Figure