Closed bannanc closed 5 years ago
Here are my comments on the docs:
API
I should have made this more clear, but the only parts of the website being updated in this PR were the API because it was affected by the code changes.
I don't want to end up with too many conflicts with PR #26 which is focused on updating the intro part of the documentation. The conda in the install is also fixed there. So I will move the checklist for the intro and installing over there. Though, the intro is being changed completely. Also in PR #26 I will make sure the code styling is consistent if you use a single accept symbol it is italicized and two accent symbols gets the color change into the "coding" format. I acknowledge there are still inconsistencies here, but I will make them all one or two accents in PR #26.
Regarding this discussion around the order of inputs.
The thought process was that input in the form [ (mol, [list of tuples] ), ... ]
would be easier for the user. However, the form for smirksify is [molecules]
[ ('label', [ [ tuples], ... ]) ]
. I don't want to make the user provide separate molecule objects for EVERY label! So actually think keeping clusters separate makes the most sense for now.
I am going to update the doc strings so there is always an example with multiple sets of tuples in one of the molecules.
The initial plan with this PR was to switch
ClusterGraph
to use tuples instead of dictionaries, but I ended up doing three things:1. Switch to tuples #37
ClusterGraph
used to expect dictionaries in the form{smirks index: atom index}
. Now it will use tuples of atom indices instead where internally the SMIRKS indices are chosen based on the order of atom indices in the tuple.That is a bond would be specified with two atoms
(0,1)
those atoms would then get SMIRKS indices:1
and:2
since there are two items in the tuple.2. Update Jupyter notebooks and Documentation API/Examples #25
Since I needed to fix ALL the code that used
ChemPerGraph
s orClusterGraph
s, I decided to also do some updating on the language around these examples in the documentation and double checked that the Jupyter notebooks were more clear.This means that PR #26 will focus on the "bigger picture" parts of the documentation webpage. Introductions, installation, and explanations on
ChemPer
is needed and what it does.3. Reorder smirksify
This is not in an issue because it occurred to me while updating the webpage stuff. I had
smirksify
in a folder calledoptimizing_smirks
. This doesn't really make sense sinceSMIRKSify
is pretty much the main function for ChemPer. I instead movedsmirksify.py
up into thechemper
folder and then movedenvironment.py
into the graphs folder, after all it is a graph based class too.