[build-system]
requires = ["setuptools<82", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "alphapulldown"
description = "Pipeline allows massive screening using alphafold"
readme = { file = "README.md", content-type = "text/markdown" }
requires-python = ">=3.8"
license = "MIT"
license-files = ["LICENSE"]
authors = [
  { name = "EMBL Hamburg", email = "alphapulldown@embl-hamburg.de" }
]
classifiers = [
  "Programming Language :: Python :: 3",
  "Operating System :: OS Independent",
]
dynamic = ["version"]
dependencies = [
  "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>=4.8.2,<5.0.0",
  "biopython>=1.81,<1.82",
  "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",
  "chex>=0.1.86",
  "immutabledict>=2.0.0",
  "typing-extensions==4.14.0",
]

[project.optional-dependencies]
alphafold2 = [
  "jax==0.5.3",
  "jax[cuda12]==0.5.3; platform_system == 'Linux' and platform_machine == 'x86_64'",
  "modelcif>=1.6",
  "numpy<2",
  "openmm>=8.2",
  "pdbfixer>=1.10",
]
alphafold3 = [
  "jaxtyping==0.2.34",
  "jax==0.5.3",
  "jax[cuda12]==0.5.3; platform_system == 'Linux' and platform_machine == 'x86_64'",
  "jax-triton==0.2.0; platform_system == 'Linux' and platform_machine == 'x86_64'",
  "modelcif>=1.6",
  "numpy<2",
  "openmm>=8.2",
  "pdbfixer>=1.10",
  "rdkit==2024.3.5",
  "triton==3.1.0; platform_system == 'Linux' and platform_machine == 'x86_64'",
  "typeguard==2.13.3",
  "zstandard",
]
test = [
  "parameterized",
  "pytest>=8.0",
  "pytest-cov>=5.0",
  "pytest-timeout>=2.3",
  "pytest-xdist>=3.6",
]

[project.urls]
Homepage = "https://github.com/KosinskiLab/AlphaPulldown"

[tool.setuptools]
include-package-data = true
packages = [
  "alphapulldown",
  "alphapulldown.utils",
  "alphapulldown.folding_backend",
  "alphapulldown.analysis_pipeline",
  "alphapulldown.scripts",
  "alphafold",
  "alphafold.data",
  "alphafold.data.tools",
  "alphafold.common",
  "alphafold.relax",
  "alphafold.model",
  "alphafold.model.geometry",
  "alphafold.model.tf",
  "alphafold.notebooks",
  "alphafold3",
  "alphafold3.structure",
  "colabfold",
  "analysis_pipeline",
  "af2plots",
  "unifold",
  "unifold.data",
  "unifold.modules",
  "unifold.msa",
  "unifold.losses",
  "unifold.symmetry",
]
script-files = [
  "./alphapulldown/scripts/create_individual_features.py",
  "./alphapulldown/scripts/run_multimer_jobs.py",
  "./alphapulldown/scripts/generate_alphafold_server_json.py",
  "./alphapulldown/analysis_pipeline/create_notebook.py",
  "./alphapulldown/analysis_pipeline/get_good_inter_pae.py",
  "./alphapulldown/analysis_pipeline/plot_diagnostics.py",
  "./alphapulldown/analysis_pipeline/plot_interaction_network.py",
  "./alphapulldown/scripts/rename_colab_search_a3m.py",
  "./alphapulldown/scripts/prepare_seq_names.py",
  "./alphapulldown/scripts/generate_crosslink_pickle.py",
  "./alphapulldown/scripts/convert_to_modelcif.py",
  "./alphapulldown/scripts/run_structure_prediction.py",
  "./alphapulldown/scripts/truncate_pickles.py",
  "./alphafold/run_alphafold.py",
]

[tool.setuptools.package-dir]
"" = "."
"alphapulldown" = "./alphapulldown"
"alphapulldown.folding_backend" = "./alphapulldown/folding_backend"
"alphafold" = "./alphafold/alphafold"
"alphafold3" = "./alphafold3/src/alphafold3"
"alphafold3.structure" = "./alphafold3/src/alphafold3/structure"
"colabfold" = "./ColabFold/colabfold"
"analysis_pipeline" = "./alphapulldown/analysis_pipeline"
"af2plots" = "./alphapulldown/analysis_pipeline/af2plots/af2plots"
"unifold" = "./AlphaLink2/unifold/"
"unifold.data" = "./AlphaLink2/unifold/data"
"unifold.losses" = "./AlphaLink2/unifold/losses"
"unifold.symmetry" = "./AlphaLink2/unifold/symmetry"

[tool.setuptools.package-data]
"alphafold.common" = ["stereo_chemical_props.txt"]

[tool.setuptools.dynamic]
version = { attr = "alphapulldown.__version__" }