MHCXGraph.core.subgraphs.compute_distmat

MHCXGraph.core.subgraphs.compute_distmat(pdb_df: pandas.DataFrame) → ndarray

Compute Euclidean distance matrix between nodes.

Multiple rows per node_id are averaged first.

Parameters:

pdb_df (pandas.DataFrame) – Must contain: [‘node_id’, ‘x_coord’, ‘y_coord’, ‘z_coord’].

Returns:

Distance matrix (N, N) in the order of first occurrence of each node_id.

Return type:

np.ndarray