mkt.databases.app.schema.StructureConfig

class mkt.databases.app.schema.StructureConfig(seq_align: SequenceAlignment, str_attr: str, 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)

Bases: ABC

Configuration for generating PyMOL files.

Uses dependency injection: receives a SequenceAlignment object which provides access to kinase info and aligned sequences.

__init__(seq_align: SequenceAlignment, str_attr: str, 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) → None

Methods

__eq__(other)	Return self==value.
__init__(seq_align, str_attr[, ...])
__post_init__()
_generate_list_idx_from_dict_align_with_attr()	Generate list of 0-indexed attribute positions from dict_align.
generate_labels(list_idx)	Generate labels for highlighted residues.
generate_list_idx()	Generate list of 0-indexed positions for the residues to be highlighted.
generate_style_color_lists(list_idx)	Generate style and color lists for StructureVisualizer based on the configuration.
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 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).
seq_align	SequenceAlignment object providing kinase info and dict_align.
str_attr	Attribute to highlight in the structure.
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, str_attr: str, 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) → None

_generate_list_idx_from_dict_align_with_attr() → list[int] | None

Generate list of 0-indexed attribute positions from dict_align.

Returns:

List of 0-indexed positions where attribute sequence has residues, or None if attribute not found in dict_align.

Return type:

list[int] | None

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

Generate labels for highlighted residues.

Override in subclasses to provide specific label formats.

Parameters:

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

Returns:

List of labels (None for residues that should not be labeled).

Return type:

list[str | None]

abstract generate_list_idx() → list[int]

Generate list of 0-indexed positions for the residues to be highlighted.

Returns:

List of 0-indexed residue positions.

Return type:

list[int]

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

Generate style and color lists for StructureVisualizer based on the configuration.

Parameters:

list_idx (list[int]) – List of 0-indexed residue positions (before +1 conversion).

Returns:

Tuple of (list_style, list_color).

Return type:

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

highlight_cartoon_transparency: float = 0.0

Cartoon transparency applied to colored/highlighted residues (0 = opaque, 1 = invisible).

label_connector: bool = True

Whether to draw leader/connector lines from each residue to its label.

label_min_dist: float = 6.0

Minimum distance (angstroms) between labels for collision avoidance.

label_offset: float = 20.0

Angstroms offset from CA for label pseudoatom placement.

label_size: int = 14

Font size for residue labels.

label_spring_strength: float = 0.0

Spring force pulling labels back toward ideal position (0 = no spring).

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__.

return_list_cif_idx() → list[int]

Return list of 0-indexed positions corresponding to the CIF sequence.

Returns:

List of 0-indexed positions where CIF sequence has residues (not gaps).

Return type:

list[int]

return_list_idx_intersect() → list[int]

Return list of 0-indexed positions at intersection of CIF and attribute sequences.

Returns:

Sorted list of 0-indexed positions present in both CIF and attribute sequences.

Return type:

list[int]

Raises:

ValueError – If attribute sequence cannot be generated from dict_align.

return_list_intersect_color_style() → tuple[list[int], list[str], list[str]]

Generate the indices, styles, and colors for highlighting.

Returns:

Tuple of (list_idx, list_color, list_style) where list_idx is 1-indexed.

Return type:

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

seq_align: SequenceAlignment

SequenceAlignment object providing kinase info and dict_align.

str_attr: str

Attribute to highlight in the structure.