Improved writing for LigninBuilder

[jvermaas]

Rather than going through the SMILES export, this is what needed to change in order to export the graph to inputs that LigninBuilder can handle. There is one big thing that I had to change, namely making bigG a directional graph from the original undirected graph. For building 3D structures, LigninBuilder links together monomers, but needs to be able to keep track of the directionality of the interaction. For undirected graphs, the edges are sorted, and the directionality is lost. The directionality is determined by the changes inside update_units, namely sorting the linkage indices. Comparing the linkage indices against the patches that apply the linkages in CHARMM gives us a straightforward output method.