cinnabar.plotting.plot_all_DDGs(graph: DiGraph, method_name: str = '', target_name: str = '', title: str = '', filename: str | None = None, plotly: bool = False, shift: float = 0.0, bootstrap_x_uncertainty: bool = False, bootstrap_y_uncertainty: bool = False, statistic_type: str = 'mle', **kwargs)[source]#

Plots relative free energies between all ligands, which is calculated from the differences between all the absolute free energies. This data is different to plot_DGs

  • graph (nx.DiGraph) – graph object with relative free energy edges

  • method_name (string, optional) – name of method associated with results, e.g. ‘perses’

  • target_name (string, optional) – name of system for results, e.g. ‘Thrombin’

  • title (string, default = ‘’) – Title for the plot

  • filename (str, default = None) – filename for plot

  • plotly (bool, default = True) – whether to use plotly for the plotting

  • shift (float, default = 0.) – shift both the x and y axis by a constant

  • bootstrap_x_uncertainty (bool, default False) – whether to account for uncertainty in x when bootstrapping

  • bootstrap_y_uncertainty (bool, default False) – whether to account for uncertainty in y when bootstrapping

  • statistic_type (str, default ‘mle’) – the type of statistic to use, either ‘mle’ (i.e. sample statistic) or ‘mean’ (i.e. bootstrapped mean statistic)