mkt.databases.app.schema.MutationsGroupConfig

class mkt.databases.app.schema.MutationsGroupConfig(seq_align: SequenceAlignment, label_offset: float = 20.0, label_min_dist: float = 6.0, label_spring_strength: float = 0.0, label_size: int = 14, label_connector: bool = True, highlight_cartoon_transparency: float = 0.0, *, str_attr: str = 'Mutations', bool_mutations_by_group: bool = True, bool_klifs_only: bool = True, bool_show_sticks: bool = False, str_filepath_json: str)

Bases: MutationsConfig

Group-averaged configuration for mutation visualization in PyMOL.

__init__(seq_align: SequenceAlignment, label_offset: float = 20.0, label_min_dist: float = 6.0, label_spring_strength: float = 0.0, label_size: int = 14, label_connector: bool = True, highlight_cartoon_transparency: float = 0.0, *, str_attr: str = 'Mutations', bool_mutations_by_group: bool = True, bool_klifs_only: bool = True, bool_show_sticks: bool = False, str_filepath_json: str) → None

Methods

__eq__(other)	Return self==value.
__init__(seq_align[, label_offset, ...])
__post_init__()
_filter_mutations_to_klifs()	Filter dict_mutations to only include residues in the 85 KLIFS pocket positions.
_generate_list_idx_from_dict_align_with_attr()	Generate list of 0-indexed attribute positions from dict_align.
_get_klifs_label(idx_0based)	Get KLIFS pocket label for a position (e.g., 'GK:45').
_get_klifs_uniprot_mapping(klifs_mapping[, ...])	Create mapping between UniProt positions and KLIFS indices.
_get_klifs_uniprot_positions(klifs_mapping)	Get the set of UniProt positions (1-indexed) in the KLIFS pocket.
_get_uniprot_label(idx_0based)	Get amino acid + UniProt position label (e.g., 'T790').
_index_mutation_region()	Extract the indices of the top mutation residues for stick highlighting.
_map_group_klifs_to_uniprot(dict_group_data)	Map group-averaged KLIFS-indexed data to target kinase's UniProt positions.
_preprocess_mutation_dict()	Preprocess mutation dictionary from JSON file.
generate_labels(list_idx)	Generate labels for top mutations: KLIFS pocket label (e.g., 'GK:45').
generate_list_idx()	Generate list of 0-indexed positions for mutation residues.
generate_style_color_lists(list_idx)	Generate style and color lists for mutation residues.
return_list_cif_idx()	Return list of 0-indexed positions corresponding to the CIF sequence.
return_list_idx_intersect()	Return list of 0-indexed positions at intersection of CIF and attribute sequences.
return_list_intersect_color_style()	Generate the indices, styles, and colors for highlighting.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
bool_klifs_only	True).
bool_mutations_by_group	True).
bool_show_sticks	False for group-averaged).
highlight_cartoon_transparency	Cartoon transparency applied to colored/highlighted residues (0 = opaque, 1 = invisible).
label_connector	Whether to draw leader/connector lines from each residue to its label.
label_min_dist	Minimum distance (angstroms) between labels for collision avoidance.
label_offset	Angstroms offset from CA for label pseudoatom placement.
label_size	Font size for residue labels.
label_spring_strength	Spring force pulling labels back toward ideal position (0 = no spring).
str_attr	'Mutations').
str_filepath_json	File path to the JSON file containing the mutation dictionary.
dict_mutations	Dictionary of mutation positions (1-indexed) with corresponding normalized counts.
seq_align	SequenceAlignment object providing kinase info and dict_align.
list_idx	List of 1-indexed residue positions to be highlighted, generated in __post_init__.
list_color	List of colors for the residues to be highlighted, generated in __post_init__.
list_style	List of styles for the residues to be highlighted, generated in __post_init__.
list_label	List of labels for the residues to be highlighted (None for no label).

__init__(seq_align: SequenceAlignment, label_offset: float = 20.0, label_min_dist: float = 6.0, label_spring_strength: float = 0.0, label_size: int = 14, label_connector: bool = True, highlight_cartoon_transparency: float = 0.0, *, str_attr: str = 'Mutations', bool_mutations_by_group: bool = True, bool_klifs_only: bool = True, bool_show_sticks: bool = False, str_filepath_json: str) → None

bool_klifs_only: bool = True

True).

Type:

Whether to only highlight KLIFS pocket residues (default

bool_mutations_by_group: bool = True

True).

Type:

Whether to average mutation counts by kinase group (default

bool_show_sticks: bool = False

False for group-averaged).

Type:

Whether to show top mutations as sticks (default

dict_mutations: dict[int, float]

Dictionary of mutation positions (1-indexed) with corresponding normalized counts.

generate_labels(list_idx: list[int]) → list[str | None]

Generate labels for top mutations: KLIFS pocket label (e.g., ‘GK:45’).

Parameters:

list_idx (list[int]) – List of 0-indexed residue positions.

Returns:

KLIFS labels for top mutation positions, None for others.

Return type:

list[str | None]

list_color: list[str]

List of colors for the residues to be highlighted, generated in __post_init__.

list_idx: list[int]

List of 1-indexed residue positions to be highlighted, generated in __post_init__.

list_label: list[str | None]

List of labels for the residues to be highlighted (None for no label).

list_style: list[str]

List of styles for the residues to be highlighted, generated in __post_init__.

seq_align: SequenceAlignment

SequenceAlignment object providing kinase info and dict_align.

str_filepath_json: str

File path to the JSON file containing the mutation dictionary.