requirements.txt

# CombFold / ColabFold extra dependencies for OneScience bio-dcu environment.
# Install with: python -m pip install --no-deps -r requirements.txt

# -----------------------------------------------------------------------------
# Provided by onescience[bio-dcu]; retained here for a complete dependency list.
# Do not install these again in the OneScience base environment.
# -----------------------------------------------------------------------------
# numpy==1.26.3
# scipy==1.14.1
# biopython==1.84
# pandas>=2.2.2
# matplotlib
# requests
# tqdm>=4.60.0
# absl-py==2.1.0
# chex==0.1.90
# dm-tree==0.1.8
# ml-collections==0.1.1
# ml-dtypes==0.4.0
# dm-haiku==0.0.14
# py3Dmol==2.5.2
# tensorflow==2.18.0+das.opt1.dtk25042
# importlib-metadata
# jax==0.4.34+das.opt1.dtk25042
# jaxlib==0.4.34+das.opt1.dtk25042
# jax-rocm60-pjrt==0.4.34+das.opt1.dtk25042
# jax-rocm60-plugin==0.4.34+das.opt1.dtk25042

# -----------------------------------------------------------------------------
# Extra Python components required by the CombFold AlphaFold-Multimer workflow.
# -----------------------------------------------------------------------------
colabfold==1.5.5
alphafold-colabfold==2.3.6
appdirs==1.4.4
immutabledict==2.2.5