finish updating WeaveModel-related stuff for restructure

Chemellia / ChemistryFeaturization.jl

Interface package for featurizing atomic structures

MIT License

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Open rkurchin opened 3 years ago

rkurchin commented 3 years ago

must-haves

[ ] get to the point of being able to build/featurize the molecule and convert it to the right format to be fed into WeaveModel.jl
[ ] figure out any other naming things, e.g. for BondFeatureDesciptors

nice-to-haves

Feel free to make a more "granular" version of this checklist, haha

thazhemadam commented 3 years ago

get to the point of being able to build/featurize the molecule and convert it to the right format to be fed into WeaveModel.jl

Does this entail something else in addition to setting up WeaveFeaturization?

some kind of visualization, maybe via OpenSMILES or MolecularGraph

This might be relatively easier to set up (wouldn't a Base.show be enough?)

rkurchin commented 3 years ago

No, I don't think it's really beyond setting that up.

Base.show should have text output in general I think; I was thinking like analogous to the graph visualization we can do for AtomGraph

rkurchin commented 3 years ago

Well I guess we may also want some convenience stuff for building commonly-desired SpeciesFeatureDescriptors

rkurchin commented 3 years ago

...which probably involves either bringing back the PyCall to rdkit or maybe playing with that jll

rkurchin commented 3 years ago

building an AtomGraph from a SMILES string etc. would also be clutch here, and make some parts of the test suite tidier too