MHCXGraph.classes.graph.Graph¶

class MHCXGraph.classes.graph.Graph(graph_path: str, config: GraphConfig)[source]¶

Graph representation of a protein structure.

This class loads a structural file (PDB or mmCIF), constructs a residue interaction graph using the configured pipeline, and provides utilities for extracting and exporting filtered subgraphs.

graph_path¶

Path to the structure file used to construct the graph.

Type:: str

config¶

Configuration object defining graph construction parameters.

Type:: GraphConfig

graph¶

Graph representation of the protein structure.

Type:: networkx.Graph

subgraphs¶

Dictionary storing named subgraphs or node selections.

Type:: dict[str, networkx.Graph | list[str]]

pdb_df¶

DataFrame containing PDB atom-level information.

Type:: pandas.DataFrame or None

raw_pdb_df¶

DataFrame containing raw PDB data before filtering.

Type:: pandas.DataFrame or None

dssp_df¶

DataFrame containing DSSP secondary structure annotations.

Type:: pandas.DataFrame or None

__init__(graph_path: str, config: GraphConfig)[source]¶

Initialize a protein structure graph.

Parameters:

graph_path (str) – Path to a PDB or mmCIF file.
config (GraphConfig) – Graph configuration object specifying node granularity, edge construction rules, and inclusion criteria for waters, ligands, and noncanonical residues.

Methods

`__init__`(graph_path, config)	Initialize a protein structure graph.
`create_subgraph`(name[, node_list, ...])	Create and store a subgraph.
`get_subgraph`(name)	Retrieve a stored subgraph by name.
`save_filtered_pdb`(g, output_path, name[, ...])	Save a filtered structural file containing only selected residues.