[WIP] Add FASTA Dataset class #289
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Reference Issues/PRs
Waiting on #272
What does this implement/fix? Explain your changes
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.
What testing did you do to verify the changes in this PR?
Pull Request Checklist
./CHANGELOG.mdfile (if applicable)./graphein/tests/*directories (if applicable)./notebooks/(if applicable)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)black .andisort .