setup.cfg

[metadata]
name = alphapulldown
author = EMBL Hamburg
author_email = alphapulldown@embl-hamburg.de
description = Pipeline allows massive screening using alphafold
url = https://github.com/KosinskiLab/AlphaPulldown
long_description = file: README.md
long_description_content_type = text/markdown
classifiers =
    Programming Language :: Python :: 3
    License :: OSI Approved :: MIT License
    Operating System :: OS Independent

[options]
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

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
include_package_data = True

python_requires = >=3.8
install_requires =
    absl-py >= 0.13.0
    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>=2.16.1
    importlib-resources>=6.1.0
    importlib-metadata>=4.8.2, <5.0.0
    biopython>=1.82
    nbformat>=5.9.2
    py3Dmol==2.0.4
    pytest>=6.0
    ipython==8.16.1
    tqdm>=4.66.1
    appdirs>=1.4.4
    jupyterlab>=3.0
    ipywidgets
    ml-dtypes
    setuptools>=40.1.0
    chex>=0.1.86
    immutabledict>=2.0.0
scripts = ./alphapulldown/scripts/create_individual_features.py
          ./alphapulldown/scripts/run_multimer_jobs.py
          ./alphapulldown/analysis_pipeline/create_notebook.py
          ./alphapulldown/analysis_pipeline/get_good_inter_pae.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

[options.package_data]
alphafold.common = stereo_chemical_props.txt