requirements.txt

# VenusREM on OneScience / Python 3.11 / DTK 25.04 / PyTorch 2.5.1
# Install this file after activating the OneScience environment.
# Active lines are the only packages that must be added or overridden.

# Required compatibility additions
# OneScience provides biotite==1.0.1, but VenusREM imports
# biotite.structure.filter_backbone, which requires the 0.41 API.
biotite==0.41.2
pathos==0.3.3

# Optional: only for generating a local residue-sequence MSA with EVcouplings.
# These are not needed for inference with the provided/precomputed A2M files.
# evcouplings==0.2.1
# hmmer==3.4.0.0
# gprofiler-official==1.0.0
# mygene==3.2.2
# plmc is an external executable, not a pip dependency.

# Provided by OneScience; retained here as the complete dependency inventory.
# Do not reinstall these generic/CUDA wheels over the DTK builds.
# torch==2.5.1                     # DTK/DCU build supplied by OneScience
# transformers==4.56.2
# numpy==1.26.3
# pandas>=2.2.2
# scipy==1.14.1
# tqdm>=4.60.0
# biopython==1.84
# joblib==1.4.2
# torch-geometric==2.7.0
# torch-scatter==2.1.0             # DTK wheel supplied by OneScience
# torch-cluster==1.6.3             # DTK wheel supplied by OneScience
# torch-sparse==0.6.18             # DTK wheel supplied by OneScience
# torch-spline-conv==1.2.2         # DTK wheel supplied by OneScience