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
[ ] 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 .
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.md
file (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 .