Integrating Flagship Pioneering protein inverse folding model (RLDIF) into bionemo

[yashaektefaie]

In the "sub-packages" directory I have added a directory called "bionemo-rldif.” In this directory is the code to run a protein inverse folding model developed by Flagship Pioneering. I added a src and test sub-directory following the structure of other projects in the "sub-packages" directory and tested this code locally and confirmed it works. Ideally users can use this code to import rldif and run our developed inverse folding model for their protein structures.

Usage

The intended usage of the code can be seen in the README of the bionemo-rldif directory. From what I saw from other packages, pip-installing the model and then importing it was the preferred usage so adapted the code to accommodate for that.

Testing

Since I don't have the AWS credentials needed to build the Docker container and the required torch-scatter package version conflicts with the PyTorch version installed by bionemo-core, I wasn't able to test the code in Docker. However, I successfully ran the test by moving the test file from the test directory to the src directory and executing:

python3 -m bionemo.rldif.test_run

This test confirms the model can generate reasonable sequences from a given pdb file, validating the core functionality.

• Did you review the Before your PR is "Ready for review" section before asking for review?

I did review this document, as stated earlier due to this AWS credential issue most of what is on there I cannot run apart from the code etiquette portion which I also left alone for now because I was not sure if that applied to this project since it is supposed to be used in a straightforward manner for model inference. If it does apply feel free to point this out and I'll comment all relevant code and functions.

• Did you make sure your changes have tests? Did you test your changes locally?

Yes, please see my response to the earlier question.

• Can you add the SKIP_CI label to your PR?

Given I was not able to test the CI cannot put this label.

• Can you add the PYTEST_NOT_REQUIRED label to your PR?

Given I was not able to run the PYTEST beyond the way I described, I cannot put this label.

• Can you add the JET_NOT_REQUIRED label to your PR?

I also cannot put this label.

[jstjohn]

/build-ci