Add helper functions to reduce reliance on format choice
Early on in development I decided to call species and reactions in certain ways,
choose certain data types and formats for fragments, edges, etc.
These helper functions are intended as a first step towards making the code less
reliant on these early decisions.
Add fragment duplicate and notation tests
Duplicate: make certain that each fragment is generated exactly once,
notation: make certain that the fragment notation reflects the edges structure
of the graph, i.e. species and reaction are aligned as edges,
there is exactly that one edge saved in the subgraph components dictionary,
the edge exists in both, digraph G and matrix alpha.
Merge branch 'develop' into develop.osx