mkt.databases.app.schema

Structure-highlighting configuration classes for the Streamlit app.

Defines the StructureConfig hierarchy (default, phosphosites, KLIFS, and mutation variants) that parameterizes how kinase structures are colored and annotated in the app.

Classes

DefaultConfig(seq_align[, label_offset, ...])	Default configuration rendering the whole protein as cartoon with spectrum coloring.
KLIFSAdaptiveConfig(seq_align, label_offset, ...)	Configuration for highlighting adaptive KLIFS residues in PyMOL.
KLIFSConfig(seq_align, label_offset, ...)	Configuration for highlighting KLIFS residues in PyMOL.
KLIFSCustomConfig(seq_align, ...)	Configuration for KLIFS regions as semi-transparent cartoon with custom stick residues.
KLIFSImportantConfig(seq_align, ...)	Configuration for highlighting important KLIFS residues in PyMOL.
KLIFSPathogenicConfig(seq_align, ...)	Configuration for highlighting KLIFS pathogenic residues in PyMOL.
KLIFSRegionLabelConfig(seq_align, ...)	Configuration for KLIFS residues with region name labels and all-ribbon representation.
MutationsConfig(seq_align[, label_offset, ...])	Configuration for generating PyMOL files with mutation data.
MutationsDefaultConfig(seq_align[, ...])	Default configuration for mutation visualization in PyMOL.
MutationsGroupConfig(seq_align[, ...])	Group-averaged configuration for mutation visualization in PyMOL.
MutationsKLIFSConfig(seq_align[, ...])	KLIFS-focused configuration for mutation visualization in PyMOL.
PhosphositesConfig(seq_align[, ...])	Configuration for highlighting phosphosites in PyMOL.
StandardConfig(value)	Enumeration of standard configurations for PyMOL visualization.
StandardConfigChoice(value)	String-based enum for CLI choices (dataclass not hashable).
StructureConfig(seq_align, str_attr[, ...])	Configuration for generating PyMOL files.

class mkt.databases.app.schema.DefaultConfig(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 = 'KinCore, CIF')

Bases: StructureConfig

Default configuration rendering the whole protein as cartoon with spectrum coloring.

__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 = 'KinCore, CIF') → None

generate_list_idx() → list[int]

Generate list of 0-indexed positions for all CIF residues.

Returns:

List of 0-indexed positions for all CIF residues.

Return type:

list[int]

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

Generate style and color lists for default spectrum coloring.

Parameters:

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

Returns:

All residues get ‘cartoon’ style and ‘spectrum’ color.

Return type:

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

str_attr: str = 'KinCore, CIF'

‘KinCore, CIF’).

Type:

Attribute to highlight in the structure (default

class mkt.databases.app.schema.KLIFSAdaptiveConfig(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>)

Bases: KLIFSConfig

Configuration for highlighting adaptive KLIFS residues in PyMOL.

__init__(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>) → None

list_stick_positions: list[int]

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

class mkt.databases.app.schema.KLIFSConfig(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>)

Bases: StructureConfig

Configuration for highlighting KLIFS residues in PyMOL.

__init__(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>) → None

_index_stick_region() → list[int]

Extract the indices of the residues in the KLIFS pocket region by removing gaps.

Returns:

List of indices for the residues in the KLIFS pocket region.

Return type:

list[int]

generate_list_idx() → list[int]

Generate list of 0-indexed positions for KLIFS residues.

Returns:

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

Return type:

list[int]

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

Generate style and color lists for KLIFS residues.

Parameters:

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

Returns:

Styles based on stick positions, colors from KLIFS pocket colors.

Return type:

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

list_stick_positions: list[int]

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

str_attr: str = 'KLIFS'

‘KLIFS’).

Type:

Attribute to highlight in the structure (default

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

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_custom_color: list[str]

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

list_uniprot_idx: list[int]

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

class mkt.databases.app.schema.KLIFSImportantConfig(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>)

Bases: KLIFSConfig

Configuration for highlighting important KLIFS residues in PyMOL.

__init__(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>) → None

list_stick_positions: list[int]

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

class mkt.databases.app.schema.KLIFSPathogenicConfig(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>)

Bases: KLIFSConfig

Configuration for highlighting KLIFS pathogenic residues in PyMOL.

__init__(seq_align: ~mkt.databases.app.sequences.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 = 'KLIFS', list_stick_positions: list[int] = <factory>) → None

list_stick_positions: list[int]

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

class mkt.databases.app.schema.KLIFSRegionLabelConfig(seq_align: ~mkt.databases.app.sequences.SequenceAlignment, label_size: int = 14, label_connector: bool = True, highlight_cartoon_transparency: float = 0.0, *, str_attr: str = 'KLIFS', label_offset: float = 12.0, label_min_dist: float = 4.5, label_spring_strength: float = 0.3, list_stick_positions: list[int] = <factory>)

Bases: KLIFSConfig

Configuration for KLIFS residues with region name labels and all-ribbon representation.

Uses KLIFS color scheme with cartoon-only styling (no sticks) and places a label at the midpoint of each KLIFS region (e.g., ‘g.l’, ‘αC’, ‘hinge’). Labels use the collision-avoidance offset logic from the PyMOL renderer.

__init__(seq_align: ~mkt.databases.app.sequences.SequenceAlignment, label_size: int = 14, label_connector: bool = True, highlight_cartoon_transparency: float = 0.0, *, str_attr: str = 'KLIFS', label_offset: float = 12.0, label_min_dist: float = 4.5, label_spring_strength: float = 0.3, list_stick_positions: list[int] = <factory>) → None

_build_align_to_klifs_mapping() → dict[int, int]

Build mapping from alignment position to KLIFS pocket position (0-indexed).

Accounts for gaps in the pocket sequence using the same logic as _index_stick_region.

Returns:

Mapping from alignment position (0-indexed) to KLIFS pocket position (0-84).

Return type:

dict[int, int]

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

Generate region name labels at the midpoint of each KLIFS region.

For each KLIFS region defined in DICT_POCKET_KLIFS_REGIONS, places a label at the alignment position closest to the region midpoint.

Parameters:

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

Returns:

Region name at midpoint positions, None for all others.

Return type:

list[str | None]

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

Generate all-cartoon style with KLIFS pocket colors.

Parameters:

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

Returns:

All residues get ‘cartoon’ style, colors from KLIFS pocket colors.

Return type:

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

label_min_dist: float = 4.5

Tighter minimum distance between region labels (angstroms).

label_offset: float = 12.0

Closer offset for region labels (angstroms).

label_spring_strength: float = 0.3

Spring force pulling labels back toward ideal position.

list_stick_positions: list[int]

No stick positions — all ribbon representation.

class mkt.databases.app.schema.MutationsConfig(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, bool_klifs_only: bool, bool_show_sticks: bool = True, str_filepath_json: str)

Bases: StructureConfig

Configuration for generating PyMOL files with mutation data.

__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, bool_klifs_only: bool, bool_show_sticks: bool = True, str_filepath_json: str) → None

_filter_mutations_to_klifs() → dict[int, float]

Filter dict_mutations to only include residues in the 85 KLIFS pocket positions.

Returns:

Filtered dictionary with only KLIFS pocket mutations.

Return type:

dict[int, float]

_get_klifs_label(idx_0based: int) → str | None

Get KLIFS pocket label for a position (e.g., ‘GK:45’).

Parameters:

idx_0based (int) – 0-indexed position in the alignment.

Returns:

KLIFS pocket label or None if not in KLIFS pocket.

Return type:

str | None

static _get_klifs_uniprot_mapping(klifs_mapping: dict | None, bool_uniprot_to_klifs: bool = True) → dict[int, int]

Create mapping between UniProt positions and KLIFS indices.

Parameters:

• klifs_mapping (dict | None) – KLIFS2UniProtIdx mapping from kinase object (ordered dict).

• bool_uniprot_to_klifs (bool, optional) – If True, return UniProt position (1-indexed) -> KLIFS index (0-84). If False, return KLIFS index (0-84) -> UniProt position (1-indexed). Default is True.

Returns:

Mapping between UniProt positions and KLIFS indices.

Return type:

dict[int, int]

static _get_klifs_uniprot_positions(klifs_mapping: dict | None) → set[int]

Get the set of UniProt positions (1-indexed) in the KLIFS pocket.

Parameters:

klifs_mapping (dict | None) – KLIFS2UniProtIdx mapping from kinase object.

Returns:

Set of 1-indexed UniProt positions in the KLIFS pocket.

Return type:

set[int]

_get_uniprot_label(idx_0based: int) → str

Get amino acid + UniProt position label (e.g., ‘T790’).

Parameters:

idx_0based (int) – 0-indexed position in the alignment.

Returns:

Label in format ‘X###’ where X is single-letter amino acid code.

Return type:

str

_index_mutation_region() → list[int]

Extract the indices of the top mutation residues for stick highlighting.

Returns:

List of 0-indexed positions for the top mutation residues.

Return type:

list[int]

_map_group_klifs_to_uniprot(dict_group_data: dict[int, float]) → dict[int, float]

Map group-averaged KLIFS-indexed data to target kinase’s UniProt positions.

Parameters:

dict_group_data (dict[int, float]) – Group-averaged normalized counts keyed by KLIFS index (0-84).

Returns:

Normalized counts mapped to target kinase’s UniProt positions (1-indexed).

Return type:

dict[int, float]

_preprocess_mutation_dict() → dict[int, float]

Preprocess mutation dictionary from JSON file.

Handles two JSON formats: - New format: {"kinases": {...}, "kinase_groups": {...}} - Legacy format: {gene_name: {pos: count, ...}, ...}

For group-averaged mode, reads pre-computed group data (keyed by KLIFS index) and maps it to the target kinase’s UniProt positions.

Returns:

Mutation dictionary with UniProt position keys (1-indexed) and normalized counts.

Return type:

dict[int, float]

bool_klifs_only: bool

Whether to only highlight KLIFS pocket residues.

bool_mutations_by_group: bool

Whether to average mutation counts by kinase group.

bool_show_sticks: bool = True

True).

Type:

Whether to show top mutations as sticks (default

dict_mutations: dict[int, float]

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

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

Generate labels for top mutation residues.

Must be implemented by subclasses to provide config-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]

generate_list_idx() → list[int]

Generate list of 0-indexed positions for mutation residues.

Returns:

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

Return type:

list[int]

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

Generate style and color lists for mutation residues.

Uses piecewise red gradient coloring: - Zero counts get lightgray - Non-zero counts are scaled piecewise and interpolated from light red to red

Parameters:

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

Returns:

Tuple of (list_style, list_color).

Return type:

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

str_attr: str = 'Mutations'

‘Mutations’).

Type:

Attribute to highlight in the structure (default

str_filepath_json: str

File path to the JSON file containing the mutation dictionary.

class mkt.databases.app.schema.MutationsDefaultConfig(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 = False, bool_klifs_only: bool = False, bool_show_sticks: bool = True, str_filepath_json: str)

Bases: MutationsConfig

Default 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 = False, bool_klifs_only: bool = False, bool_show_sticks: bool = True, str_filepath_json: str) → None

bool_klifs_only: bool = False

False).

Type:

Whether to only highlight KLIFS pocket residues (default

bool_mutations_by_group: bool = False

False).

Type:

Whether to average mutation counts by kinase group (default

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

Generate labels for top mutations: amino acid + UniProt position (e.g., ‘T790’).

Parameters:

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

Returns:

Labels for top mutation positions, None for others.

Return type:

list[str | None]

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

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

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]

class mkt.databases.app.schema.MutationsKLIFSConfig(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 = False, bool_klifs_only: bool = True, bool_show_sticks: bool = True, str_filepath_json: str)

Bases: MutationsConfig

KLIFS-focused 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 = False, bool_klifs_only: bool = True, bool_show_sticks: bool = True, 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 = False

False).

Type:

Whether to average mutation counts by kinase group (default

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

Generate labels for top mutations: KLIFS label + amino acid + UniProt position.

Example: ‘GK:45 T790’

Parameters:

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

Returns:

Combined KLIFS + UniProt labels for top mutation positions, None for others.

Return type:

list[str | None]

class mkt.databases.app.schema.PhosphositesConfig(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 = 'Phosphosites')

Bases: StructureConfig

Configuration for highlighting phosphosites 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 = 'Phosphosites') → None

generate_list_idx() → list[int]

Generate list of 0-indexed positions for phosphosite residues.

Returns:

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

Return type:

list[int]

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

Generate style and color lists for phosphosites.

Parameters:

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

Returns:

All residues get ‘stick’ style and ‘red’ color.

Return type:

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

str_attr: str = 'Phosphosites'

‘Phosphosites’).

Type:

Attribute to highlight in the structure (default

class mkt.databases.app.schema.StandardConfig(value)

Bases: Enum

Enumeration of standard configurations for PyMOL visualization.

DEFAULT = <class 'mkt.databases.app.schema.DefaultConfig'>

KLIFS_ADAPTIVE = <class 'mkt.databases.app.schema.KLIFSAdaptiveConfig'>

KLIFS_CUSTOM = <class 'mkt.databases.app.schema.KLIFSCustomConfig'>

KLIFS_IMPORTANT = <class 'mkt.databases.app.schema.KLIFSImportantConfig'>

KLIFS_PATHOGENIC = <class 'mkt.databases.app.schema.KLIFSPathogenicConfig'>

KLIFS_REGION_LABEL = <class 'mkt.databases.app.schema.KLIFSRegionLabelConfig'>

MUTATIONS_DEFAULT = <class 'mkt.databases.app.schema.MutationsDefaultConfig'>

MUTATIONS_GROUP = <class 'mkt.databases.app.schema.MutationsGroupConfig'>

MUTATIONS_KLIFS = <class 'mkt.databases.app.schema.MutationsKLIFSConfig'>

PHOSPHOSITES = <class 'mkt.databases.app.schema.PhosphositesConfig'>

class mkt.databases.app.schema.StandardConfigChoice(value)

Bases: str, Enum

String-based enum for CLI choices (dataclass not hashable).

DEFAULT = 'DEFAULT'

KLIFS_ADAPTIVE = 'KLIFS_ADAPTIVE'

KLIFS_CUSTOM = 'KLIFS_CUSTOM'

KLIFS_IMPORTANT = 'KLIFS_IMPORTANT'

KLIFS_PATHOGENIC = 'KLIFS_PATHOGENIC'

KLIFS_REGION_LABEL = 'KLIFS_REGION_LABEL'

MUTATIONS_DEFAULT = 'MUTATIONS_DEFAULT'

MUTATIONS_GROUP = 'MUTATIONS_GROUP'

MUTATIONS_KLIFS = 'MUTATIONS_KLIFS'

PHOSPHOSITES = 'PHOSPHOSITES'

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

_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.