| # 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 | |