graphein [WIP] Add FASTA Dataset class

[WIP] Add FASTA Dataset class

Open a-r-j opened this issue 2 years ago • 1 comments

Waiting on #272

Dataset class for working with Sequence Datasets. Provides utilities for batch folding and embedding with ESM(Fold).

[ ] Set representative structure. For protein engineering tasks we can have a setup where we predict a single WT structure, which we use as the structure for the mutants & simply appropriately modify the residue types.
[] FoldComp compression of the predicted structures. Ideally this would run in the ESMFold step, but we can also do it post-hoc.

[ ] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
[ ] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
[ ] Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
[ ] Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
[ ] Checked for style issues by running black . and isort .