plot_DDGs#

cinnabar.plotting.plot_DDGs(femap: FEMap, source: str, method_name: str = '', target_name: str = '', title: str = '', map_positive: bool = False, filename: str | None = None, symmetrise: bool = False, plotly: bool = False, data_label_type: Literal['small-molecule', 'protein-mutation'] | None=None, 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]#

Function to plot relative free energies

Parameters:

  • femap (FEMap) – FEMap object with relative and absolute free energy edges

  • source (str) – The source label of the computational relative free energies to plot against experiment. This must match the source field used when the calculations were added to the FEMap. For data loaded via FEMap.from_csv (or added without an explicit source), pass source="".

  • 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”.

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

  • map_positive (bool, default False) – Whether to map all DDGs to the positive x values. This is an aesthetic choice

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

  • symmetrise (bool, default False) – Whether to plot each datapoint twice, both positive and negative values.

  • plotly (bool, default False) – Whether to use plotly to generate the plot.

  • data_label_type ({“small-molecule”, “protein-mutation”} | None, default None) – Type of data label to add to each edge

    if None data labels will not be added

    if 'small-molecule' edge labels will be f"{node_A_name}→{node_B_name}".

    if 'protein-mutation' edge labels will given as single letter amino acid codes separated by the mutated residue index (eg. "Y29A")

    If both node names start with "-", the negative sign will be factored out (eg. "-(Y29A)" or "-(benzene→toluene)").

    currently unsupported for plotly-generated plots

  • 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".

Return type:

Nothing

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