Ecstasy

Benchmarking different models in protein design.

Setup

1. Setting up the environment

Clone the repository with submodules:

git submodule update --init --recursive

3.1. Installing Ecstasy Base Environment

bash scripts/install/ecstasy.sh

3.2. Installing ESMFold

bash scripts/install/esmfold.sh

3.3. Installing Boltz

bash scripts/install/boltz.sh

3.4. Installing ColabFold

bash scripts/install/colabfold.sh

[DEV] Management of Repository

Maintaning dependencies

To add a package to primary dependencies in UV pyproject.toml, run: uv add <package-name>

To add an optional dependency to the dev group in UV pyproject.toml, run: uv add <package-name> --optional dev

Managing submodules

To add a new submodule, run:

git submodule add <repository-url> <path-to-submodule>

Managing Tests

To only run ecstasy tests, run (from the root of the repository):

uv run pytest tests/

UV for Submodules

Create venv using:

uv venv envs/boltz && source envs/boltz/bin/activate

Install dependencies using:

uv pip install -e modules/boltz