mkt.databases.pymol.PyMOLGenerator

class mkt.databases.pymol.PyMOLGenerator(viz: ~mkt.databases.app.structures.StructureVisualizer, str_attr: str, dict_filenames: dict = <factory>)[source]

Bases: object

Generate PDB file with embedded color/style info and standalone PyMOL script.

__init__(viz: ~mkt.databases.app.structures.StructureVisualizer, str_attr: str, dict_filenames: dict = <factory>) → None

Methods

`__eq__`(other)	Return self==value.
`__init__`(viz, str_attr[, dict_filenames])
`__post_init__`()
`_convert_color_to_hex`(color)	Convert named color to hex, with fallback options.
`_get_color_and_style_mapping`()	Generate residue-to-color mapping, stick residue list, and label mapping.
`generate_annotated_pdb`(output_path)	Generate PDB file with renumbered residues and color/style annotations.
`generate_instructions`(output_dir)	Generate instructions for manual PyMOL execution.
`generate_pymol_script`(pdb_path, output_path)	Generate PyMOL script that reads annotations from PDB and applies styling.
`return_filepath_dict`(output_dir)	Return dictionary of filenames with paths.
`save_pymol_files`(output_dir)	Generate PDB file and PyMOL script for manual PyMOL execution.

Attributes

`__dataclass_fields__`
`__dataclass_params__`
`__match_args__`
`viz`	StructureVisualizer object with loaded structure and config.
`str_attr`	Granular attribute name of the structure visualization (e.g., KLIFS_IMPORTANT not just KLIFS).
`gene_name`	Gene name of the structure.
`dict_filenames`	Dictionary of filenames for PDB, script, and instructions.

__init__(viz: ~mkt.databases.app.structures.StructureVisualizer, str_attr: str, dict_filenames: dict = <factory>) → None

_convert_color_to_hex(color: str) → str[source]

Convert named color to hex, with fallback options.

Parameters:: color (str) – Color name or hex string.
Returns:: Hex color string.
Return type:: str

_get_color_and_style_mapping() → tuple[dict[int, str], list[int], dict[int, str]][source]

Generate residue-to-color mapping, stick residue list, and label mapping.

Uses the get_highlight_data() from StructureVisualizer which gets data from the config.

Returns:: Dictionary mapping residue numbers to hex colors, list of stick residue numbers, dictionary mapping residue numbers to label strings.
Return type:: tuple[dict[int, str], list[int], dict[int, str]]

dict_filenames: dict: Dictionary of filenames for PDB, script, and instructions.

gene_name: str: Gene name of the structure.

generate_annotated_pdb(output_path: str) → str[source]

Generate PDB file with renumbered residues and color/style annotations.

Parameters:: output_path (str) – Path to save the annotated PDB file.
Returns:: Path to the saved annotated PDB file.
Return type:: str

generate_instructions(output_dir: str) → str[source]

Generate instructions for manual PyMOL execution.

Parameters:: output_dir (str) – Directory where files are saved
Returns:: Instructions text
Return type:: str

generate_pymol_script(pdb_path: str, output_path: str) → str[source]

Generate PyMOL script that reads annotations from PDB and applies styling.

Parameters:

pdb_path (str) – Path to the annotated PDB file.
output_path (str) – Path to save the PyMOL script.

Returns:

Path to the saved PyMOL script.

Return type:

str

return_filepath_dict(output_dir: str) → dict[str, str][source]

Return dictionary of filenames with paths.

Parameters:: output_dir (str) – Directory where files are saved.
Returns:: Dictionary mapping file types to full file paths.
Return type:: dict[str, str]

save_pymol_files(output_dir: str)[source]

Generate PDB file and PyMOL script for manual PyMOL execution.

Parameters:: output_dir (str) – Directory to save files

str_attr: str: Granular attribute name of the structure visualization (e.g., KLIFS_IMPORTANT not just KLIFS).

viz: StructureVisualizer: StructureVisualizer object with loaded structure and config.