quemb.molbe.graphfrag.GraphGenUtility.get_subgraphs

static GraphGenUtility.get_subgraphs(motifs_per_frag, edge_list, origin_per_frag, adx_map, fdx=None, options={})

Construct labeled subgraphs for fragments using motif, edge, and label data.

If a fragment index (fdx) is provided, returns a dictionary containing the subgraph for that single fragment. Otherwise, returns a dictionary of subgraphs for all fragments, keyed by their respective fragment indices (fdx).

Parameters:

  • motifs_per_frag (list[Sequence[int]]) – A list where each item is a sequence of node indices (motifs) per fragment.

  • edge_list (list[Sequence]) – A list of edge groupings, each corresponding to a fragment’s set of edges.

  • origin_per_frag (list[Sequence[int]]) – A list where each item is a sequence of node indices marking origin nodes within each fragment.

  • adx_map (dict) – A mapping from node index to metadata, where each value must contain a “label” field for node annotation.

  • fdx (int | None) – Index of a specific fragment to extract. If None (default), subgraphs for all fragments are returned.

  • options (dict) – Optional keyword arguments passed to the nx.Graph constructor for each subgraph.

Returns:

subgraph_dict – a dictionary mapping fragment indices to networkx.graph objects. If fdx is given, the dictionary will contain only one entry for that fragment.

Return type:

dict

Notes

  • Origin nodes are highlighted by enclosing their labels in square brackets.

  • Returned graphs include labeled nodes and edges per fragment.

  • The structure and labels are derived from adx_map and origin_per_frag.