chore: Remove small molecule test species

[trisyoungs]

Removes yet more code-constructed test species and converts them to TOML. Also adds Species::load() to load a species directly, useful in unit tests.

This work removes most of the usages of modifying functions in the Species class, making refactor it a lot easier!

[RobBuchananCompPhys]

Suggested change

	auto name = contents["species"]["name"].as_string();
	setName(name.str);
	if (contents.contains("species"))
	deserialise(contents["species"])

I feel that my preference would be to have the species name set inside deserialise - this would contain the responsibility to fully initialise the species from TOML within a single method.

Then, this would become ^

Is there any reason we don't do this already?

[trisyoungs]

To be honest I've been ignoring this a bit, but ultimately the Species class doesn't need a name_ member as this should be the SpeciesNode name. However, the relationship between those two things is not quite clear to me at present. I agree that the name could / should be set in the deserialise(), so I'll make that change.