helix-hive

Agentic Collaborative Protein Engineer

Steps to Setup the Repo

1. Install uv - brew install uv (or the equivalent for Linux/Windows)
2. uv venv --python $(which python)
3. Ensure that the .python-version file has the appropriate python version - might cause failures if the global python version is different from the python version for the current venv (mentioned in the pyproject.toml) file
   • Additionally, torchtext isn't currently supported with py3.13. Hence python<=3.12 is required
4. uv sync
5. brew install muscle

Testing components one by one

Retrieval Agent

1. make index
   • build a sample index from data/examples/small.fasta
2. make query
3. Test Queries

# Build index
uv run python -m agents.retriever build --fasta data/examples/small.fasta

# Run query
uv run python -m agents.retriever query --seq MKTAYIAKQRQISFVKSHFSRQDILDLWQ --k 5

# Build MSA with Clustal Omega (default)
uv run python -m agents.retriever msa --seq MKTAYIAKQRQISFVKSHFSRQDILDLWQ --k 5

# Build MSA with MAFFT
uv run python -m agents.retriever msa --seq MKTAYIAKQRQISFVKSHFSRQDILDLWQ --k 5 --tool mafft

Design Agent

1. make design