mkt.databases.app.structures.StructureVisualizer

class mkt.databases.app.structures.StructureVisualizer(config: StructureConfig)[source]

Bases: object

Load and process kinase structures for visualization.

This class handles structure loading from KinaseInfo CIF data and provides highlight data for visualization. Style/color logic is delegated to StructureConfig objects.

Parameters:

config (StructureConfig) – Configuration object containing seq_align (with kinase info) and pre-computed list_idx, list_color, list_style for highlighting.

Variables:

config (StructureConfig) – The configuration object.
obj_kinase (KinaseInfo) – KinaseInfo object from config.seq_align.obj_kinase.
structure (Structure) – Bio.PDB Structure object loaded from CIF.
pdb_text (str) – PDB-formatted string of the structure.
residues (list) – List of residues from the structure.

__init__(config: StructureConfig)[source]

Methods

`__eq__`(value, /)	Return self==value.
`__init__`(config)
`_convert_mmcifdict2structure`()	Convert this kinase's MMCIF2Dict to a Bio.PDB Structure.
`_convert_structure2string`()	Convert this Bio.PDB Structure object to a PDB format string.
`_generate_highlight_idx`()	Alias for get_highlight_data() for backwards compatibility.
`get_highlight_data`()	Get highlight indices and color/style/label dictionaries for visualization.
`parse_pdb_line`(line)	Parse a line from a PDB file and extract relevant information.

__init__(config: StructureConfig)[source]

_convert_mmcifdict2structure() → Structure[source]

Convert this kinase’s MMCIF2Dict to a Bio.PDB Structure.

Returns:: Bio.PDB Structure object.
Return type:: Structure

_convert_structure2string() → str[source]

Convert this Bio.PDB Structure object to a PDB format string.

Returns:: Structure in PDB string format.
Return type:: str

_generate_highlight_idx() → tuple[list[int], dict[int, str], dict[int, str], dict[int, str | None]][source]: Alias for get_highlight_data() for backwards compatibility.

Deprecated since version Use: get_highlight_data() instead.

get_highlight_data() → tuple[list[int], dict[int, str], dict[int, str], dict[int, str | None]][source]

Get highlight indices and color/style/label dictionaries for visualization.

The config provides list_idx (1-indexed), list_color, list_style, and list_label. This method converts them to the dict format expected by consumers.

Returns:

list_highlight: List of 1-indexed residue positions to highlight.
dict_color: Mapping from residue position to color.
dict_style: Mapping from residue position to style.
dict_label: Mapping from residue position to label (None for no label).

Return type:

tuple[list[int], dict[int, str], dict[int, str], dict[int, str | None]]

static parse_pdb_line(line: str) → dict[str, Any] | None[source]

Parse a line from a PDB file and extract relevant information.

Parameters:: line (str) – Line from a PDB file.
Returns:: Dictionary containing extracted information or None if the line does not match the criteria (ATOM line with CA atom).
Return type:: dict[str, Any] | None