mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
4d802be7d6
* symmetrical refactoring to support both af2 and af3 data pipelines * Clean tests * Keep GPU tests in place * Reverted accidentally deleted templates * Add AlphaFold3 feature creation pipeline and per-chain input generation - Implement `create_pipeline_af3` to construct the AlphaFold3 data pipeline with correct database and binary paths. - Add `create_af3_individual_features` to generate AlphaFold3 input features for each chain in a FASTA, handling protein, RNA, and DNA sequences. - Integrate new AF3 logic into the main entry point, dispatching to AF2 or AF3 as appropriate. - Ensure output directory creation and error handling for missing dependencies or invalid sequences. * Convert template dates to datetime for af3 * First check for nucleotides, then for amino-acids * Skip existing features json if --skip_existing=true * Check if DNA before RNA * Bump 2.1.0 * Git ignore build/ dir
97 lines
2.8 KiB
INI
97 lines
2.8 KiB
INI
[metadata]
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name = alphapulldown
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author = EMBL Hamburg
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author_email = alphapulldown@embl-hamburg.de
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description = Pipeline allows massive screening using alphafold
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url = https://github.com/KosinskiLab/AlphaPulldown
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long_description = file: README.md
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long_description_content_type = text/markdown
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classifiers =
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Programming Language :: Python :: 3
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License :: OSI Approved :: MIT License
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Operating System :: OS Independent
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[options]
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packages=
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alphapulldown
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alphapulldown.utils
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alphapulldown.folding_backend
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alphapulldown.analysis_pipeline
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alphapulldown.scripts
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alphafold
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alphafold.data
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alphafold.data.tools
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alphafold.common
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alphafold.relax
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alphafold.model
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alphafold.model.geometry
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alphafold.model.tf
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alphafold.notebooks
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alphafold3
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alphafold3.structure
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colabfold
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analysis_pipeline
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af2plots
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unifold
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unifold.data
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unifold.modules
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unifold.msa
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unifold.losses
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unifold.symmetry
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package_dir =
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alphapulldown = ./alphapulldown
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alphapulldown.folding_backend = ./alphapulldown/folding_backend
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alphafold = ./alphafold/alphafold
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alphafold3 = ./alphafold3/src/alphafold3
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alphafold3.structure = ./alphafold3/src/alphafold3/structure
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colabfold = ./ColabFold/colabfold
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analysis_pipeline = ./alphapulldown/analysis_pipeline
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af2plots = ./alphapulldown/analysis_pipeline/af2plots/af2plots
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unifold = ./AlphaLink2/unifold/
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unifold.data = ./AlphaLink2/unifold/data
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unifold.losses = ./AlphaLink2/unifold/losses
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unifold.symmetry = ./AlphaLink2/unifold/symmetry
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include_package_data = True
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python_requires = >=3.8
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install_requires =
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absl-py >= 0.13.0
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dm-haiku
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dm-tree>=0.1.6
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h5py>=3.1.0
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matplotlib>=3.3.3
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ml-collections>=0.1.0
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pandas>=1.5.3
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tensorflow-cpu>=2.16.1
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importlib-resources>=6.1.0
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importlib-metadata>=4.8.2, <5.0.0
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biopython>=1.82
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nbformat>=5.9.2
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py3Dmol==2.0.4
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pytest>=6.0
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parameterized
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ipython==8.16.1
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tqdm>=4.66.1
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appdirs>=1.4.4
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jupyterlab>=3.0
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ipywidgets
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ml-dtypes
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setuptools>=40.1.0
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chex>=0.1.86
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immutabledict>=2.0.0
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scripts = ./alphapulldown/scripts/create_individual_features.py
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./alphapulldown/scripts/run_multimer_jobs.py
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./alphapulldown/analysis_pipeline/create_notebook.py
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./alphapulldown/analysis_pipeline/get_good_inter_pae.py
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./alphapulldown/scripts/rename_colab_search_a3m.py
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./alphapulldown/scripts/prepare_seq_names.py
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./alphapulldown/scripts/generate_crosslink_pickle.py
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./alphapulldown/scripts/convert_to_modelcif.py
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./alphapulldown/scripts/run_structure_prediction.py
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./alphapulldown/scripts/truncate_pickles.py
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./alphafold/run_alphafold.py
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[options.package_data]
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alphafold.common = stereo_chemical_props.txt
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