MHCXGraph.utils.preprocessing

exception MHCXGraph.utils.preprocessing.LogicError

Bases: Exception

Raised when a logical selection expression cannot be evaluated.

MHCXGraph.utils.preprocessing.collect_selected_files_from_manifest(manifest)

Collect structure files defined in the manifest input rules.

Parameters:

manifest (dict) – Manifest configuration dictionary.

Returns:

selected_files – List of dictionaries describing selected input files.

Return type:

list[dict]

MHCXGraph.utils.preprocessing.create_graphs(manifest: dict) → list[tuple]

Construct filtered graphs from the manifest input structures.

The function loads structure files, builds graph representations, applies residue selection filters, and stores intermediate outputs.

Parameters:

manifest (dict) – Manifest configuration dictionary containing runtime settings and input selection rules.

Returns:

graphs – List of tuples containing the filtered graph, original file path, and base structure name.

Return type:

list[tuple]

MHCXGraph.utils.preprocessing.get_exposed_residues(graph: Graph, rsa_filter: float, asa_filter: float, selection_params=None) → Graph

Generate a filtered subgraph containing exposed residues.

The function creates a residue subgraph based on solvent exposure criteria and optional structural or logical filters defined in the manifest.

Parameters:

• graph (Graph) – Graph representation of the protein structure.

• rsa_filter (float) – Relative solvent accessibility threshold.

• asa_filter (float) – Absolute solvent accessibility threshold.

• selection_params (dict[str, Any], optional) – Additional selection constraints such as chains, residues, secondary structure elements, or logical expressions.

Returns:

subgraph – Filtered graph containing the selected residues.

Return type:

networkx.Graph

Raises:

Exception – If no residues satisfy the filtering conditions.

MHCXGraph.utils.preprocessing.list_struct_files(folder: Path, extensions: list[str]) → list[Path]

Recursively list structure files inside a directory.

Parameters:

• folder (pathlib.Path) – Root directory to search.

• extensions (list[str]) – Allowed file extensions.

Returns:

files – Sorted list of structure file paths.

Return type:

list[pathlib.Path]

MHCXGraph.utils.preprocessing.resolve_selection_params_for_file(file_path: Path, manifest: dict[str, Any]) → dict[str, Any]

Resolve selection parameters for a specific input file.

Parameters:

• file_path (pathlib.Path) – Path to the structure file.

• manifest (dict[str, Any]) – Manifest configuration.

Returns:

params – Combined selector parameters applied to the file.

Return type:

dict[str, Any]

Functions

collect_selected_files_from_manifest(manifest)	Collect structure files defined in the manifest input rules.
create_graphs(manifest)	Construct filtered graphs from the manifest input structures.
get_exposed_residues(graph, rsa_filter, ...)	Generate a filtered subgraph containing exposed residues.
list_struct_files(folder, extensions)	Recursively list structure files inside a directory.
resolve_selection_params_for_file(file_path, ...)	Resolve selection parameters for a specific input file.

Exceptions

LogicError

Raised when a logical selection expression cannot be evaluated.