pyemap.process_data.create_graph

pyemap.process_data.create_graph(dmatrix, node_labels, edge_prune, coef_alpha, exp_beta, r_offset, distance_cutoff, percent_edges, num_st_dev_edges, max_degree, eta_moieties)[source]

Constructs the graph from the distance matrix and node labels.

Parameters:

  • dmatrix (numpy.array of float) – Distance matrix of aromatic residues.

  • node_label (list of str) – Labels for residues in the graph.

  • edge_prune (int) – 0 for degree, 1 for percent

  • residue_numbers – res numbers

  • distance_cutoff (float) – Parameters that determine which edges are kept.

  • max_degree (float) – Parameters that determine which edges are kept.

  • eta_moieties (list of str) – Non standard residues that were automatically identified

Returns:

G – Graph of aromatic residues in protein

Return type:

networkx.Graph

References

Gray, H. B.; Winkler, J. R. Long-Range Electron Transfer. Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (10),

3534 LP-3539. Reference for 20A filter on edges