BioSimSpace.Align.generateNetwork

BioSimSpace.Align.generateNetwork(molecules, names=None, work_dir=None, plot_network=False)

Generate a perturbation network using Lead Optimisation Mappper (LOMAP).

Parameters

• molecules (:[class:Molecule]) – A list of molecules.

• names ([str]) – A list of names for the molecules. If None, then the index of each molecule will be used.

• work_dir (str) – The working directory for the LOMAP process.

• plot_network (bool) – Whether to plot the network when running from within a notebook.

Returns

• edges ([(int, int)]) – A tuple containing the edges of the network. Each edge is itself a tuple, containing the indices of the molecules that are connected by the edge.

• scores ([float]) – The LOMAP score for each edge. The higher the score implies that a perturbation between molecules along an edge is likely to be more accurate.