mkt.databases.app.schema.KLIFSCustomConfig

class mkt.databases.app.schema.KLIFSCustomConfig(seq_align: ~mkt.databases.app.sequences.SequenceAlignment, label_spring_strength: float = 0.0, *, str_attr: str = 'KLIFS', label_offset: float = 4.0, label_min_dist: float = 0.0, label_size: int = 24, label_connector: bool = False, highlight_cartoon_transparency: float = 0.3, list_stick_positions: list[int] = <factory>, list_uniprot_idx: list[int] = <factory>, list_custom_color: list[str] = <factory>)

Bases: KLIFSConfig

Configuration for KLIFS regions as semi-transparent cartoon with custom stick residues.

Renders all KLIFS pocket residues as pocket-colored, slightly transparent cartoon and overlays a user-supplied set of full-length UniProt positions as opaque sticks in user-supplied colors.

__init__(seq_align: ~mkt.databases.app.sequences.SequenceAlignment, label_spring_strength: float = 0.0, *, str_attr: str = 'KLIFS', label_offset: float = 4.0, label_min_dist: float = 0.0, label_size: int = 24, label_connector: bool = False, highlight_cartoon_transparency: float = 0.3, list_stick_positions: list[int] = <factory>, list_uniprot_idx: list[int] = <factory>, list_custom_color: list[str] = <factory>) → None

Methods

__eq__(other)	Return self==value.
__init__(seq_align[, label_spring_strength, ...])
__post_init__()
_generate_list_idx_from_dict_align_with_attr()	Generate list of 0-indexed attribute positions from dict_align.
_index_stick_region()	Extract the indices of the residues in the KLIFS pocket region by removing gaps.
generate_labels(list_idx)	Generate amino acid + UniProt position labels for the custom stick residues.
generate_list_idx()	Generate 0-indexed positions for KLIFS pocket residues plus custom positions.
generate_style_color_lists(list_idx)	Generate style and color lists for KLIFS regions and custom 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__
highlight_cartoon_transparency	Cartoon transparency for the colored KLIFS regions (0 = opaque, 1 = invisible).
label_connector	No leader lines for the zoomed pocket view.
label_min_dist	No collision repulsion between the few custom labels.
label_offset	Small offset (angstroms) so the label sits next to its residue.
label_size	Larger font for the zoomed pocket view.
label_spring_strength	Spring force pulling labels back toward ideal position (0 = no spring).
str_attr	'KLIFS').
list_uniprot_idx	List of 1-indexed full-length UniProt positions to highlight as sticks.
list_custom_color	List of colors corresponding to list_uniprot_idx (must be the same length).
list_stick_positions	List of 0-indexed positions in KLIFS sequence for stick representation.
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: ~mkt.databases.app.sequences.SequenceAlignment, label_spring_strength: float = 0.0, *, str_attr: str = 'KLIFS', label_offset: float = 4.0, label_min_dist: float = 0.0, label_size: int = 24, label_connector: bool = False, highlight_cartoon_transparency: float = 0.3, list_stick_positions: list[int] = <factory>, list_uniprot_idx: list[int] = <factory>, list_custom_color: list[str] = <factory>) → None

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

Generate amino acid + UniProt position labels for the custom stick residues.

Parameters:

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

Returns:

Label ‘X###’ (e.g., ‘T790’, single-letter amino acid + 1-indexed UniProt position) for custom positions, None for KLIFS-only positions.

Return type:

list[str | None]

generate_list_idx() → list[int]

Generate 0-indexed positions for KLIFS pocket residues plus custom positions.

Returns:

Sorted union of 0-indexed KLIFS pocket residues (present in the CIF) and custom UniProt positions (1-indexed input converted to 0-indexed), filtered to those present in the KinCore CIF structure.

Return type:

list[int]

generate_style_color_lists(list_idx: list[int]) → tuple[list[str], list[str]]

Generate style and color lists for KLIFS regions and custom residues.

Parameters:

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

Returns:

Custom positions get ‘stick’ style and their supplied color; all other (KLIFS) positions get ‘cartoon’ style and their KLIFS pocket color.

Return type:

tuple[list[str], list[str]]

highlight_cartoon_transparency: float = 0.3

Cartoon transparency for the colored KLIFS regions (0 = opaque, 1 = invisible).

label_connector: bool = False

No leader lines for the zoomed pocket view.

label_min_dist: float = 0.0

No collision repulsion between the few custom labels.

label_offset: float = 4.0

Small offset (angstroms) so the label sits next to its residue.

label_size: int = 24

Larger font for the zoomed pocket view.

list_color: list[str]

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

list_custom_color: list[str]

List of colors corresponding to list_uniprot_idx (must be the same length).

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_stick_positions: list[int]

List of 0-indexed positions in KLIFS sequence for stick representation.

list_style: list[str]

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

list_uniprot_idx: list[int]

List of 1-indexed full-length UniProt positions to highlight as sticks.

seq_align: SequenceAlignment

SequenceAlignment object providing kinase info and dict_align.