mkt.databases.app.utils.create_structure_visualizer

mkt.databases.app.utils.create_structure_visualizer(seq_align: SequenceAlignment, config_class: type[StructureConfig], config_kwargs: dict | None = None) → StructureVisualizer[source]

Create a StructureVisualizer from a SequenceAlignment and config class.

This is the recommended way to create a StructureVisualizer with the new architecture. The flow is: 1. Create SequenceAlignment 2. Pass it to this function with a config class 3. Get back a StructureVisualizer ready for visualization

Parameters:

seq_align (SequenceAlignment) – SequenceAlignment object with aligned sequences.
config_class (Type[StructureConfig]) – The config class to instantiate (e.g., PhosphositesConfig, KLIFSConservedConfig).
config_kwargs (dict | None, optional) – Additional keyword arguments to pass to the config class, by default None.

Returns:

StructureVisualizer object ready for visualization.

Return type:

StructureVisualizer

Examples

>>> from mkt.databases.app.sequences import SequenceAlignment
>>> from mkt.databases.app.schema import PhosphositesConfig
>>>
>>> # Create sequence alignment
>>> seq_align = SequenceAlignment(str_kinase="EGFR", dict_color={"A": "blue", ...})
>>>
>>> # Create structure visualizer
>>> viz = create_structure_visualizer(seq_align, PhosphositesConfig)
>>>
>>> # Get highlight data
>>> list_idx, dict_color, dict_style = viz.get_highlight_data()