├── .github └── workflows │ ├── publish.yaml │ └── tests.yaml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin ├── reduce └── smina.static ├── changelog.md ├── data ├── crossdocked_split_by_name.pkl ├── examples │ ├── 1a2g.pdb │ └── 1a2g_ligand.sdf ├── posecheck_logo.png └── split_by_name.pt ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── index.rst │ └── posecheck_logo.png ├── posecheck ├── .DS_Store ├── __init__.py ├── data │ ├── __init__.py │ └── datasets.py ├── docking_eval.py ├── eval.py ├── posecheck.py └── utils │ ├── __init__.py │ ├── biopython.py │ ├── chem.py │ ├── clashes.py │ ├── constants.py │ ├── docking.py │ ├── docking_utils.py │ ├── interactions.py │ ├── loading.py │ ├── strain.py │ └── validators.py ├── requirements.txt ├── setup.py └── tests ├── __init__.py ├── test_biopython.py ├── test_chem.py ├── test_clashes.py ├── test_hydride.py ├── test_interactions.py ├── test_loading.py ├── test_posecheck.py └── test_strain.py /.github/workflows/publish.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/.github/workflows/publish.yaml -------------------------------------------------------------------------------- /.github/workflows/tests.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/.github/workflows/tests.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include requirements.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/README.md -------------------------------------------------------------------------------- /bin/reduce: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/bin/reduce -------------------------------------------------------------------------------- /bin/smina.static: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/bin/smina.static -------------------------------------------------------------------------------- /changelog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/changelog.md -------------------------------------------------------------------------------- /data/crossdocked_split_by_name.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/data/crossdocked_split_by_name.pkl -------------------------------------------------------------------------------- /data/examples/1a2g.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/data/examples/1a2g.pdb -------------------------------------------------------------------------------- /data/examples/1a2g_ligand.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/data/examples/1a2g_ligand.sdf -------------------------------------------------------------------------------- /data/posecheck_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/data/posecheck_logo.png -------------------------------------------------------------------------------- /data/split_by_name.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/data/split_by_name.pt -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/posecheck_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/docs/source/posecheck_logo.png -------------------------------------------------------------------------------- /posecheck/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/.DS_Store -------------------------------------------------------------------------------- /posecheck/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/__init__.py -------------------------------------------------------------------------------- /posecheck/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /posecheck/data/datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/data/datasets.py -------------------------------------------------------------------------------- /posecheck/docking_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/docking_eval.py -------------------------------------------------------------------------------- /posecheck/eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/eval.py -------------------------------------------------------------------------------- /posecheck/posecheck.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/posecheck.py -------------------------------------------------------------------------------- /posecheck/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /posecheck/utils/biopython.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/biopython.py -------------------------------------------------------------------------------- /posecheck/utils/chem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/chem.py -------------------------------------------------------------------------------- /posecheck/utils/clashes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/clashes.py -------------------------------------------------------------------------------- /posecheck/utils/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/constants.py -------------------------------------------------------------------------------- /posecheck/utils/docking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/docking.py -------------------------------------------------------------------------------- /posecheck/utils/docking_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/docking_utils.py -------------------------------------------------------------------------------- /posecheck/utils/interactions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/interactions.py -------------------------------------------------------------------------------- /posecheck/utils/loading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/loading.py -------------------------------------------------------------------------------- /posecheck/utils/strain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/strain.py -------------------------------------------------------------------------------- /posecheck/utils/validators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/posecheck/utils/validators.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/setup.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_biopython.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_biopython.py -------------------------------------------------------------------------------- /tests/test_chem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_chem.py -------------------------------------------------------------------------------- /tests/test_clashes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_clashes.py -------------------------------------------------------------------------------- /tests/test_hydride.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_hydride.py -------------------------------------------------------------------------------- /tests/test_interactions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_interactions.py -------------------------------------------------------------------------------- /tests/test_loading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_loading.py -------------------------------------------------------------------------------- /tests/test_posecheck.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_posecheck.py -------------------------------------------------------------------------------- /tests/test_strain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cch1999/posecheck/HEAD/tests/test_strain.py --------------------------------------------------------------------------------