ovo.core.logic.proteinqc_logic

Module Contents

Functions

tool_supports_scheduler
get_available_schedulers	Get available schedulers based on the tools selected by the user.
get_available_tools	Get available tools based on the selected scheduler.
get_descriptor_plot_setting	Get the thresholds, reverse_colors and color_by settings for the descriptor plot.
get_descriptor_colormap	Create a matplotlib colormap and normalization object corresponding to the Altair redyellowgreen scheme with 4 points in the domain as specified by the thresholds.
get_plddt_color	Create a color function for pLDDT values based on standard thresholds.
get_pae_colormap	Create a color function for PAE values.
get_rmsd_colormap	Create a color function for RMSD values.
get_higher_is_better_colormap
get_lower_is_better_colormap
get_neutral_colormap
get_descriptor_cmap	Return a color mapping function for the given descriptor.
get_flag_color
get_descriptor_comment

API

ovo.core.logic.proteinqc_logic.tool_supports_scheduler(tool: ovo.core.database.models_proteinqc.ProteinQCTool, scheduler: ovo.core.scheduler.base_scheduler.Scheduler) → bool

ovo.core.logic.proteinqc_logic.get_available_schedulers(tools: List[ovo.core.database.models_proteinqc.ProteinQCTool]) → dict[str, ovo.core.scheduler.base_scheduler.Scheduler]

Get available schedulers based on the tools selected by the user.

ovo.core.logic.proteinqc_logic.get_available_tools(tools: List[ovo.core.database.models_proteinqc.ProteinQCTool], scheduler: ovo.core.scheduler.base_scheduler.Scheduler) → List[ovo.core.database.models_proteinqc.ProteinQCTool]

Get available tools based on the selected scheduler.

ovo.core.logic.proteinqc_logic.get_descriptor_plot_setting(descriptor: ovo.core.database.Descriptor) → Tuple[List[float], bool, str]

Get the thresholds, reverse_colors and color_by settings for the descriptor plot.

The logic for thresholds is as follows:

• For descriptors with ‘lower_is_better’, thresholds are [min_value, warning_value, error_value, max_value].

• For descriptors with ‘higher_is_better’, thresholds are [min_value, error_value, warning_value, max_value].

• If any of these values are not set (i.e., None), thresholds will be None.

Returns: Tuple[List[float], bool, str]: thresholds, reverse_colors, color_by

ovo.core.logic.proteinqc_logic.get_descriptor_colormap(thresholds: List[float], reverse_colors: bool = False, colors=None)

Create a matplotlib colormap and normalization object corresponding to the Altair redyellowgreen scheme with 4 points in the domain as specified by the thresholds.

Args: thresholds (List[float]): List of threshold values to define color transitions. reverse_colors (bool): If True, reverse the color order.

Returns: Callable[[float], str]: A function that takes a value and returns a hex color string of a color in the colormap.

ovo.core.logic.proteinqc_logic.get_plddt_color(thresholds: List[float] = [90, 70, 50], lighter: bool = False)

Create a color function for pLDDT values based on standard thresholds.

> 90, very high confidence, ‘#0053d6’

> 70, high confidence, ‘#65cbf3’

> 50, low confidence, ‘#ffdb13’

< 50, ‘Very low confidence’, ‘#ff7d45’

ovo.core.logic.proteinqc_logic.get_pae_colormap()

Create a color function for PAE values.

ovo.core.logic.proteinqc_logic.get_rmsd_colormap()

Create a color function for RMSD values.

ovo.core.logic.proteinqc_logic.get_higher_is_better_colormap(min_val, max_val)

ovo.core.logic.proteinqc_logic.get_lower_is_better_colormap(min_val, max_val)

ovo.core.logic.proteinqc_logic.get_neutral_colormap(min_val, max_val)

ovo.core.logic.proteinqc_logic.get_descriptor_cmap(descriptor: ovo.core.database.Descriptor, min_val: float, max_val: float)

Return a color mapping function for the given descriptor.

Colormap logic:

• For special descriptors (e.g., pLDDT, PAE), apply custom color schemes.

• If all thresholds (min_value, warning_value, error_value, max_value) are set, use them for color transitions based on the comparison type.

• If thresholds are not fully set but a comparison is defined, use a 2-color scale (more green is better) based on comparison type and min/max values in the data.

• If thresholds are not fully set and no comparison is defined, use a neutral colormap (higher values are darker grey), determined by min/max values in the data.

Args: descriptor (Descriptor): The descriptor for which to create the colormap. min_val (float): Minimum value among the selected designs. max_val (float): Maximum value among the selected designs.

ovo.core.logic.proteinqc_logic.get_flag_color(value: float, descriptor: ovo.core.database.Descriptor) → Literal[green, yellow, orange, missing, None]

ovo.core.logic.proteinqc_logic.get_descriptor_comment(descriptor: ovo.core.database.Descriptor) → str