Closed davidlmobley closed 5 years ago
@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.
I'm including these in PR #29
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.
Taking a quick look at the chemper docs on chemper.readthedocs.io, I see a few issues:
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 thesmirks_dict
). Also you introduce tehlayers
option without explaining it.ClusterGraph
: Somewhat the same issue; it's a bit hard to understand exactly whatsmirks_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 itdicts
and notdict
?layers
requires more explanation and it could be made more clear what you're trying to do and why.I think that's it. Overall there's a sense that the big picture is not clear yet.