absl-py>=0.13.0
alphapulldown-input-parser>=0.5.0
dm-haiku
dm-tree>=0.1.6
h5py>=3.1.0
matplotlib>=3.3.3
ml-collections>=0.1.0
pandas>=1.5.3
tensorflow-cpu==2.20.0
importlib-resources>=6.1.0
importlib-metadata<5.0.0,>=4.8.2
biopython<1.82,>=1.81
nbformat>=5.9.2
py3Dmol==2.0.4
ipython==8.16.1
tqdm>=4.66.1
appdirs>=1.4.4
jupyterlab>=3.0
ipywidgets
ml-dtypes
immutabledict>=2.0.0
typing-extensions>=4.15.0

[alphafold2]
jax==0.5.3
modelcif>=1.6
numpy<2
openmm>=8.2
pdbfixer>=1.10

[alphafold2:platform_system == "Linux" and platform_machine == "x86_64"]
jax[cuda12]==0.5.3

[alphafold3]
dm-haiku==0.0.16
jax==0.9.1
modelcif>=1.6
numpy
openmm>=8.2
pdbfixer>=1.10
rdkit==2025.9.4
tokamax==0.0.11
zstandard

[alphafold3:platform_system == "Linux" and platform_machine == "x86_64"]
jax[cuda12]==0.9.1

[test]
parameterized
pytest>=8.0
pytest-cov>=5.0
pytest-timeout>=2.3
pytest-xdist>=3.6
