├── .coveragerc ├── .github └── workflows │ ├── ci.yml │ └── publish.yml ├── .gitignore ├── .readthedocs.yml ├── LICENSE.txt ├── README.rst ├── doc ├── Makefile └── source │ ├── _static │ └── ritalin3d.png │ ├── _templates │ └── layout.html │ ├── api │ ├── e3fp.config.params.rst │ ├── e3fp.config.rst │ ├── e3fp.conformer.generate.rst │ ├── e3fp.conformer.generator.rst │ ├── e3fp.conformer.protonation.rst │ ├── e3fp.conformer.rst │ ├── e3fp.conformer.util.rst │ ├── e3fp.fingerprint.array_ops.rst │ ├── e3fp.fingerprint.db.rst │ ├── e3fp.fingerprint.fprint.rst │ ├── e3fp.fingerprint.fprinter.rst │ ├── e3fp.fingerprint.generate.rst │ ├── e3fp.fingerprint.metrics.array_metrics.rst │ ├── e3fp.fingerprint.metrics.fprint_metrics.rst │ ├── e3fp.fingerprint.metrics.rst │ ├── e3fp.fingerprint.rst │ ├── e3fp.fingerprint.structs.rst │ ├── e3fp.fingerprint.util.rst │ ├── e3fp.pipeline.rst │ ├── e3fp.rst │ ├── e3fp.util.rst │ └── index.rst │ ├── conf.py │ ├── dev │ └── index.rst │ ├── examples │ └── data │ │ ├── caffeine.smi │ │ ├── new_params.cfg │ │ └── test_smiles.smi │ ├── index.rst │ ├── install.rst │ ├── overview.rst │ ├── substitutions.rst │ └── usage │ ├── cli.rst │ ├── config.rst │ ├── fingerprints │ ├── comparison.rst │ ├── fprints.rst │ ├── index.rst │ └── storage.rst │ ├── index.rst │ └── pipeline.rst ├── pyproject.toml ├── pytest.ini ├── src └── e3fp │ ├── __init__.py │ ├── config │ ├── __init__.py │ ├── defaults.cfg │ └── params.py │ ├── conformer │ ├── __init__.py │ ├── generate.py │ ├── generator.py │ ├── protonation.py │ └── util.py │ ├── fingerprint │ ├── __init__.py │ ├── array_ops.py │ ├── db.py │ ├── fprint.py │ ├── fprinter.py │ ├── generate.py │ ├── metrics │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── array_metrics._dense_soergel-225.py312.1.nbc │ │ │ ├── array_metrics._dense_soergel-225.py312.nbi │ │ │ ├── array_metrics._sparse_soergel-246.py312.1.nbc │ │ │ └── array_metrics._sparse_soergel-246.py312.nbi │ │ ├── array_metrics.py │ │ └── fprint_metrics.py │ ├── structs.py │ └── util.py │ ├── pipeline.py │ └── util.py └── tests ├── __init__.py ├── data ├── caffeine_planar.sdf.bz2 ├── rand_sdf_files │ ├── CHEMBL116226.sdf.bz2 │ ├── CHEMBL197946.sdf.bz2 │ ├── CHEMBL2114064.sdf.bz2 │ ├── CHEMBL282186.sdf.bz2 │ └── CHEMBL501745.sdf.bz2 ├── ritalin_nonplanar.sdf ├── ritalin_nonplanar.sdf.bz2 ├── stereo1.sdf.bz2 └── stereo2.sdf.bz2 ├── test_config.py ├── test_conformer.py ├── test_dependencies.py ├── test_fingerprint.py ├── test_fingerprinting.py ├── test_fprint_db.py ├── test_metrics.py ├── test_struct.py └── test_util.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/keiserlab/e3fp/HEAD/.coveragerc -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- 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