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Chemellia / ChemistryFeaturization.jl

Interface package for featurizing atomic structures
https://chemistryfeaturization.chemellia.org/dev/
MIT License
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basic atomic feat and bond feat functions #1

Closed SeanXiaoyuSun closed 4 years ago

SeanXiaoyuSun commented 4 years ago

Basic functions are ported in this PR. Tested with manually checking return values of some sample molecules
Atom and Bond struct were deleted for more flexible features selection. atom_features() and bond_features() now return dictionary of feature onehot vectors or values. I think this could make it easier to merge with CGCNN featurizer. We can concatenate dictionaries from both part and convert the integrated dictionary to a feature matrix before returning to user.

rkurchin commented 4 years ago

Looks great! Can you write up the tests and add them to SMILES_tests.jl? (Look up some documentation for writing/running unit tests if you're unfamiliar, you can start from here) If you need to add some sample files to test on, just make a subdirectory in the tests folder for that for now.

(you may have to pull my latest commit to get the updated testing files too)

SeanXiaoyuSun commented 4 years ago

@rkurchin I just pushed the update of my part. Can you check if my part is consistent with yours?