plot_all_DDGs#

cinnabar.plotting.plot_all_DDGs(femap: FEMap, source: str, 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: Literal['mle', 'mean']='mle', observable_type: Literal['ddg', 'dpic50']='ddg', temperature: Quantity = <Quantity(298.15, 'kelvin')>, **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.

Parameters:

  • femap (FEMap) – FEMap object with absolute free energies to plot.

  • source (str) – The name of the source label of the computational absolute values, if absolute values are generated with the MLE estimator this should be “MLE”.

  • method_name (string, default “”) – Name of method associated with results, e.g. “openfe” by default an empty string.

  • target_name (string, default “”) – Name of system for results, e.g. “Thrombin” by default an empty string.

  • title (string, default “”) – Title for the plot.

  • filename (str | None, default None) – Filename for plot if None the plot will be displayed.

  • 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 ({“mle”, “mean”}, default “mle”) – The type of statistic to use, either “mle” (i.e. sample statistic) or “mean” (i.e. bootstrapped mean statistic).

  • observable_type ({“ddg”, “dpic50”}, default “ddg”) – The observable type to plot values in. Defaults to ddg (kcal/mol). Use dpic50 to plot DpIC50 values.

  • temperature (Quantity, default 298.15 * unit.kelvin) – Temperature used for the unit conversion, only used if observable_type is "dpic50".

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