MAINT: create `KineticDiagram` object and move relevant functions into class body about kda HOT 2 CLOSED

I've thought about this a bit more, and there may be some downsides to creating a new object for storing all of the info. The networkx.MultiDiGraph() object offers quite a bit of features that may be worth keeping, so it may be better to keep everything within that object instead of making our own. We could inherit its methods into our own object instead, but there may be some reasons not to do that either. Whatever gets us an easy-to-use interface without losing all of the well-developed NetworkX methods will take the cake.

Before moving forward it would be worthwhile to review other similar objects and see how others are handling similar situations. The MDAnalysis.Universe object comes to mind.

from kda.