├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── auglichem ├── __init__.py ├── crystal │ ├── __init__.py │ ├── _transforms.py │ ├── data │ │ ├── __init__.py │ │ ├── _crystal_dataset.py │ │ ├── _knn.py │ │ └── _load_sets.py │ └── models │ │ ├── __init__.py │ │ ├── _radius_graph.py │ │ ├── cgcnn.py │ │ ├── gcn.py │ │ ├── gin.py │ │ └── schnet.py ├── molecule │ ├── __init__.py │ ├── _compositions.py │ ├── _transforms.py │ ├── data │ │ ├── __init__.py │ │ ├── _load_sets.py │ │ └── _molecule_dataset.py │ └── models │ │ ├── __init__.py │ │ ├── afp.py │ │ ├── deepgcn.py │ │ ├── gcn.py │ │ └── gine.py ├── test │ ├── test_crystal.py │ ├── test_molecule.py │ └── test_utils.py └── utils │ ├── __init__.py │ ├── _constants.py │ └── _splitting.py ├── codecov.yml ├── docs ├── .DS_Store ├── Gemfile ├── Gemfile.lock ├── README.md ├── _config.yml ├── _includes │ ├── disqus_comments.html │ ├── footer.html │ ├── google-analytics.html │ ├── head.html │ ├── header.html │ ├── search.html │ ├── sidebar.html │ └── social.html ├── _layouts │ ├── default.html │ ├── home.html │ ├── page.html │ ├── post.html │ └── search.html ├── _posts │ ├── 2021-11-29-release.md │ ├── 2022-1-19-update.md │ ├── 2022-11-10-publication.md │ ├── 2022-4-11-custom dataset.md │ ├── 2022-5-16-update.md │ └── 2024-2-13-update.md ├── _sass │ ├── minima.scss │ └── minima │ │ ├── _base.scss │ │ ├── _layout.scss │ │ └── _syntax-highlighting.scss ├── about.md ├── assets │ ├── jekyll.png │ ├── main.scss │ ├── minima-social-icons.svg │ └── search.json ├── crystal.md ├── crystal_usage.md ├── images │ ├── .DS_Store │ ├── Nacl.png │ ├── Nacl_numbered.png │ ├── Nacl_perturb.png │ ├── Nacl_rotate.png │ ├── Nacl_super.png │ ├── Nacl_swapped.png │ ├── Nacl_translate.png │ ├── Picture1.png │ ├── Picture2.png │ ├── Picture3.png │ ├── Picture4.png │ ├── Picture5.png │ ├── Project.png │ ├── crystal_augment.png │ ├── crystal_pipeline.png │ ├── data_loading_pipeline.png │ ├── logo.png │ ├── methane.png │ ├── molecule_augment.pdf │ ├── molecule_augment.png │ ├── molecule_pipeline.png │ ├── motif.png │ └── original_molecule.png ├── install_guide.md ├── jekyll-readthedocs.gemspec ├── logo.png ├── molecule.md ├── molecule_usage.md └── search.html ├── examples ├── crystal_cgcnn_dataset.ipynb ├── crystal_cgcnn_kfold_dataset.ipynb ├── crystal_dataset.ipynb ├── crystal_kfold_dataset.ipynb ├── molecule_dataset.ipynb └── molecule_multitarget_dataset.ipynb ├── pyproject.toml └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.vscode 2 | *__pycache__ 3 | *.swp 4 | */data_download/ 5 | _site/ 6 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BaratiLab/AugLiChem/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: 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