Consistency/Consolidation in Parsing Methods

[pbauman]

Some methods we take a pointer to a parser that's already created (e.g. ChemicalMixture constructor). Others, we don't give that option and construct the parser internally (e.g. `read_reaction_set_data1). It would be nice for the user to instantiate one parser object and use it everywhere, if appropriate.

[pbauman]

There are some methods that live in global namespace, e.g. read_reaction_set_data, that should be in ParserBase and then calls methods that can be implemented in subclasses. This is once example. We definitely want to consolidate all these because the parsing is spread out everywhere making it really hard to follow.