MHCXGraph.core.pdb_graph_builder.BuiltGraph¶

class MHCXGraph.core.pdb_graph_builder.BuiltGraph(graph: nx.Graph, residue_index: list[tuple[str, Residue]], residue_centroids: np.ndarray, water_index: list[tuple[str, Residue]] = <factory>, water_centroids: np.ndarray | None = None, distance_matrix: np.ndarray | None = None, raw_pdb_df: pd.DataFrame | None = None, node_centroids: pd.DataFrame | None = None, dssp_df: pd.DataFrame | None = None)[source]¶

Container returned by PDBGraphBuilder.

graph¶

Constructed graph with node/edge attributes.

Type:: networkx.Graph

residue_index¶

Node id to residue pairing for amino acid residues used as the main distance base.

Type:: list of tuple[str, Bio.PDB.Residue]

residue_centroids¶

Centroids for residue_index in the same order, shape (N, 3).

Type:: numpy.ndarray

water_index¶

Node id to residue pairing for water residues (if included).

Type:: list of tuple[str, Bio.PDB.Residue]

water_centroids¶

Water centroids in the same order as water_index, shape (W, 3).

Type:: numpy.ndarray or None

distance_matrix¶

Pairwise centroid distance matrix for residues in residue_index.

Type:: numpy.ndarray or None

raw_pdb_df¶

Atom-level table used to derive centroids and CA/CB coordinates.

Type:: pandas.DataFrame or None

node_centroids¶

DataFrame indexed by node_id with centroid coordinates x_coord, y_coord, z_coord.

Type:: pandas.DataFrame or None

dssp_df¶

DSSP summary with an added “rsa” column, aligned to graph nodes.

Type:: pandas.DataFrame or None

__init__(graph: nx.Graph, residue_index: list[tuple[str, Residue]], residue_centroids: np.ndarray, water_index: list[tuple[str, Residue]] = <factory>, water_centroids: np.ndarray | None = None, distance_matrix: np.ndarray | None = None, raw_pdb_df: pd.DataFrame | None = None, node_centroids: pd.DataFrame | None = None, dssp_df: pd.DataFrame | None = None) → None¶

Methods

__init__(graph, residue_index, Residue]], ...)

Attributes

`distance_matrix`
`dssp_df`
`node_centroids`
`raw_pdb_df`
`water_centroids`
`graph`
`residue_index`
`residue_centroids`
`water_index`