String & Graph Assembly indices

[colemathis]

Assembly Indices can be computed for things besides molecules, the most interesting use cases are character strings (like UUGAGTTGCACC), or graph objects.

Generalizing the code to handle these would be a significant improvement. Optimizing the branch/bound techniques and the canonization for these classes would be an improvement over the state of the art.

[jdaymude]

After a conversation with @AgentElement and @Garrett-Pz, we want to:

• Modify all public assembly::* endpoints to take petgraph::Graphs instead of Molecules.
• Refactor the molecule module to be one among several input graph types (creating the possibility to add other loaders).
• Update all the documentation to talk about graphs in general instead of molecules.

@colemathis has started something on the beyond-molecules branch; we'll take a look at that as well.