requests>=2.28
tqdm>=4.64
numpy>=1.24
click>=8.1
pyyaml>=6.0
colorlog>=6.7
biopython>=1.81
scipy>=1.10
scikit-learn>=1.3

[all]
proteinfp[structure]
proteinfp[ml]
proteinfp[chem]
proteinfp[grn]
proteinfp[sim]

[chem]
rdkit>=2023.3

[dev]
pytest>=7.4
pytest-cov>=4.1
black>=23.0
ruff>=0.1
mypy>=1.5

[grn]
scanpy>=1.9
anndata>=0.9

[ml]
torch>=2.0
xgboost>=2.0
lightgbm>=4.0
fair-esm>=2.0

[sim]
openmm>=8.0

[structure]
freesasa>=2.1
