quemb.molbe.graphfrag.GraphGenUtility.export_graph

static GraphGenUtility.export_graph(edge_list, adx_map, adjacency_graph, origin_per_frag, dnames, outdir=None, outname='AdjGraph', cmap='cubehelix', node_position='coordinates')

Export a visual representation of a fragment-based adjacency graph to a PNG.

This function draws a directed network graph using a provided adjacency structure, with fragments color-coded and displayed using either coordinate-based or spring-layout node positioning, and saves the resulting image to the specified output directory.

Parameters:

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

  • adx_map (dict) – Mapping from node indices to node metadata (must include ‘coord’ and ‘label’ keys).

  • adjacency_graph (Graph) – The NetworkX graph containing node and edge connectivity.

  • origin_per_frag (list[Sequence[int]]) – A list of node index groups, each corresponding to the origin nodes of a fragment.

  • dnames (list[str]) – Names for each fragment, used in the legend.

  • outdir (Path | None) – If specified as Path: export .png to outdir. If None: no .png is exported, but (fix, ax) are still returned.

  • outname (str) – Filename (without extension) for the output image. Default is “AdjGraph”.

  • cmap (str) – Matplotlib colormap name used to color-code fragments. Default is “cubehelix”.

  • node_position (str) – Node positioning strategy: “coordinates” for z-shifted spatial coordinates, or “spring” for force-directed layout. Default is “coordinates”.

Returns:

(fix, ax) – Returns the corresponding pyplot objects.

Return type:

tuple[object, object]

Notes

  • Assumes that adx_map contains a “coord” field for all nodes: [x, y, z] coordinates when using “coordinates” positioning.

  • Colors are assigned per fragment based on the chosen colormap.

  • Nodes are drawn in two layers to produce a bordered effect.

  • Arcs between nodes are radially offset to distinguish overlapping edges.