Doc cleanup

[davidlmobley]

Taking a quick look at the chemper docs on chemper.readthedocs.io, I see a few issues:

• [x] API page: "chemper is open source if you have suggestions or concerns please add them to our issue tracker. Below is an outline of tools provided in chemper see examples for more details." That should be two sentences or should have a semicolon.
• [x] API page: "While this isn’t ultimately useful in sampling chemical perception as they only work for a single molecule, however it is a tool that did not exist to the best of the authors knowledge before"; grammar needs help. Also "The indexed atoms are the two carbon atoms at indices 0 and 1 in the molecule are assigned to SMIRKS indices..." There are two "are"'s but only one subject.
• [x] API on chemperGraph; I think it could be made more clear which atoms are which in the dictionary (e.g. the first atom in the SMILES string is atom 1?) and what exactly is happening (e.g. what functionality is triggered by the smirks_dict). Also you introduce teh layers option without explaining it.
• [x] API on ClusterGraph: Somewhat the same issue; it's a bit hard to understand exactly what smirks_dicts is doing/what data structure it's using. It looks like a list of lists, but both lists only have one entry? Why? And why is it dicts and not dict?
• [x] The "Examples" seem to recapitulate material from the Jupyter notebooks; on "Single molecule SMIRKS" I have the same comments as the jupyter notebooks, especially that layers requires more explanation and it could be made more clear what you're trying to do and why.
• [x] The "Make SMIRKS from clustered subgraphs" example refers to "this notebook", which is odd since it's not a notebook; as Jessica and I also noted there is the word "ethan" there.
• [x] "What's next" has the word "innputs".

I think that's it. Overall there's a sense that the big picture is not clear yet.

[bannanc]

@davidlmobley I updated your list to be a checklist so I can check things off when I've completed them. After Jessica and I talked I had basically planned to rewrite the intro page completely to be more big picture and then only focused on chemper. I'll move the smarty/smirky stuff to somewhere else for people who might want to read it, maybe make a Previous Work or Related Work section, let me know if you have a good idea for the name of that section.

The "Make SMIRKS from clustered subgraphs" example refers to "this notebook", which is odd since it's not a notebook

So this page is automatically generated from the example jupyter notebooks (super handy readthedocs thing), probably the best thing to do is to refer to notebooks as "in this example" inside the notebooks so it makes more sense on the website.

[bannanc]

I'm including these in PR #29

[bannanc]

Actually, I've reordered a few things on my todo list, I've included the API points and example comments in PR #41. I am going to close this issue when that is accepted and make a new issue with my personal checklist for the introduction points.