biobagel 0.1.1

Protein Engineering via Exploration of an Energy Landscape

BAGEL: Protein Engineering via Exploration of an Energy Landscape

Installation

From PyPI (Recommended)

The easiest way to install BAGEL is through PyPI:

pip install biobagel

Optional Extras:

• For local protein model execution (requires GPU):

pip install biobagel[local]

• For development (testing, linting, documentation):

pip install biobagel[dev]

From Source

If you want to install from source or contribute to development:

1. Clone the repository:

git clone https://github.com/softnanolab/bagel

2. Install uv (if not already installed):

curl -LsSf https://astral.sh/uv/install.sh | sh

3. Navigate to the repository:

cd bagel

4. Install the environment:

uv sync

Optional Extras:

• For local protein model execution (requires GPU):

uv sync --extra local

• For development (testing, linting, documentation):

uv sync --extra dev

• For all extras:

uv sync --all-extras

Usage

With PyPI Installation

python scripts/script.py

With Source Installation

uv run python scripts/script.py

To execute templates reliably from the technical report manuscript [citation to be added], follow release v0.1.0, also stored on Zenodo.

Oracles

One can either run Oracles locally, or remotely.

• use_modal=True: Run Oracles on Modal. Using the boileroom package, running remotely is made seamless and does not require installing any dependencies. However, you need to have credits to use Modal.
• use_modal=False: Run Oracles locally through boileroom. You need a GPU with suitable memory requirements.

To use Modal, one needs to create an account and authenticate through:

    modal token new

You also need to set HF_MODEL_DIR to an accessible folder, where HuggingFace models will be stored.

Examples

Templates and example applications from the manuscript are included as ready-to-run Python scripts.

Contributing

For development setup, testing, and contribution guidelines, see Development Guide.