Comments (5)
thazhemadam
commented on July 23, 2024
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?)
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rkurchin
commented on July 23, 2024
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
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rkurchin
commented on July 23, 2024
Well I guess we may also want some convenience stuff for building commonly-desired SpeciesFeatureDescriptors
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rkurchin
commented on July 23, 2024
...which probably involves either bringing back the PyCall to rdkit or maybe playing with that jll
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rkurchin
commented on July 23, 2024
building an AtomGraph from a SMILES string etc. would also be clutch here, and make some parts of the test suite tidier too
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Related Issues (20)
- #92 might not be a sustainable fix HOT 1
- move `output_file_path` to positional arguments in `AtomGraph` constructor from file
- PyCall may be a CI hurdle HOT 4
- `visualize(::AtomGraph)` should write to file HOT 1
- `AtomGraph`s can't be built from files if a relative path is provided
- Using strings to create Featurizations via GraphNodeFeaturization doesn't work with things other than ElementFeatureDescriptors HOT 1
- Change from DiffEqBase to SciMLBase HOT 1
- make `featurization` in `FeaturizedAtoms` a `const` once Julia 1.8 is released
- Coulomb Matrix featurization
- Use Intervals.jl in onehot-decode
- some `ElementFeature` convenience functions HOT 5
- make `SpeciesFeature` implementations, tests HOT 9
- fix macOS CI HOT 2
- make `DummyFeaturization` HOT 1
- make a `validate_features` function
- make `validate_features` function HOT 1
- custom broadcast for featurize
- improve/expand tests for FeaturizedAtoms, encoding HOT 2
- pretty printing for `FeaturizedAtoms`
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