├── .coveragerc ├── .gitignore ├── .scrutinizer.yml ├── .travis.yml ├── LICENSE ├── README.md ├── ci ├── .fuelrc ├── environment.yml └── install.sh ├── conda.yaml ├── conftest.py ├── docs ├── Makefile ├── _static │ └── css │ │ └── custom.css ├── _templates │ └── layout.html ├── api │ ├── modules.rst │ ├── skchem.core.rst │ ├── skchem.cross_validation.rst │ ├── skchem.data.converters.rst │ ├── skchem.data.datasets.rst │ ├── skchem.data.downloaders.rst │ ├── skchem.data.rst │ ├── skchem.descriptors.rst │ ├── skchem.filters.rst │ ├── skchem.forcefields.rst │ ├── skchem.interact.rst │ ├── skchem.io.rst │ ├── skchem.pandas_ext.rst │ ├── skchem.pipeline.rst │ ├── skchem.resource.rst │ ├── skchem.rst │ ├── skchem.standardizers.rst │ ├── skchem.test.rst │ ├── skchem.test.test_cross_validation.rst │ ├── skchem.test.test_data.rst │ ├── skchem.test.test_filters.rst │ ├── skchem.test.test_io.rst │ ├── skchem.test.test_standardizers.rst │ ├── skchem.utils.rst │ └── skchem.vis.rst ├── conf.py ├── developing.rst ├── index.rst ├── installing.rst ├── introduction.rst ├── make.bat ├── navbar.py ├── quickstart.ipynb ├── releases │ ├── v0.0.6.rst │ └── v0.0.7.rst ├── tutorial.rst ├── tutorial │ ├── data.ipynb │ ├── filters.ipynb │ ├── io.ipynb │ ├── molecules.ipynb │ ├── package.ipynb │ ├── pipelines.ipynb │ └── transformers.ipynb └── whatsnew.rst ├── environment.yml ├── pylintrc ├── readthedocs.yml ├── requirements.txt ├── scripts └── convert.py ├── setup.cfg ├── setup.py ├── skchem ├── __init__.py ├── base.py ├── core │ ├── __init__.py │ ├── atom.py │ ├── base.py │ ├── bond.py │ ├── conformer.py │ └── mol.py ├── cross_validation │ ├── __init__.py │ └── similarity_threshold.py ├── data │ ├── .DS_Store │ ├── __init__.py │ ├── converters │ │ ├── __init__.py │ │ ├── base.py │ │ ├── bradley_open_mp.py │ │ ├── bursi_ames.py │ │ ├── chembl.py │ │ ├── diversity_set.py │ │ ├── muller_ames.py │ │ ├── nmrshiftdb2.py │ │ ├── physprop.py │ │ └── tox21.py │ ├── datasets │ │ ├── __init__.py │ │ ├── base.py │ │ ├── bradley_open_mp.py │ │ ├── bursi_ames.py │ │ ├── chembl.py │ │ ├── diversity_set.py │ │ ├── muller_ames.py │ │ ├── nmrshiftdb2.py │ │ ├── physprop.py │ │ └── tox21.py │ └── downloaders │ │ ├── __init__.py │ │ ├── base.py │ │ ├── bradley_open_mp.py │ │ ├── bursi_ames.py │ │ ├── chembl.py │ │ ├── diversity.py │ │ ├── muller_ames.py │ │ ├── nmrshiftdb2.py │ │ ├── physprop.py │ │ └── tox21.py ├── features │ ├── __init__.py │ ├── atom.py │ ├── chemaxon.py │ ├── descriptors │ │ ├── __init__.py │ │ ├── autocorrelation.py │ │ ├── caching.py │ │ ├── charge.py │ │ ├── constitutional.py │ │ └── fundamentals.py │ ├── fingerprints.py │ ├── moe.py │ └── physicochemical.py ├── filters │ ├── __init__.py │ ├── base.py │ ├── simple.py │ ├── smarts.py │ └── stereo.py ├── forcefields │ ├── __init__.py │ ├── base.py │ ├── mmff.py │ └── uff.py ├── interact │ ├── __init__.py │ └── desc_vis.py ├── io │ ├── __init__.py │ ├── objects.py │ ├── sdf.py │ └── smiles.py ├── metrics.py ├── pandas_ext │ ├── __init__.py │ └── structure_methods.py ├── pipeline │ ├── __init__.py │ └── pipeline.py ├── resource │ ├── __init__.py │ ├── atom_data.csv │ ├── methane.smiles │ ├── test_sdf │ │ ├── multi_molecule-bad_chemistry.sdf │ │ ├── multi_molecule-bad_structure.sdf │ │ ├── multi_molecule-properties.sdf │ │ ├── multi_molecule-simple.sdf │ │ ├── single_molecule-properties.sdf │ │ └── single_molecule-simple.sdf │ └── test_smiles │ │ ├── custom_header.smiles │ │ ├── header_set.smiles │ │ ├── multi_molecule-bad_chemistry.smiles │ │ ├── multi_molecule-bad_smiles.smiles │ │ ├── multi_molecule-properties.smiles │ │ ├── multi_molecule-simple.smiles │ │ ├── name_set.smiles │ │ ├── sep_changed.smiles │ │ ├── single_molecule.smiles │ │ └── smiles_col_changed.smiles ├── standardizers │ ├── __init__.py │ ├── chemaxon.py │ └── default_config.xml ├── test │ ├── __init__.py │ ├── test_core │ │ ├── __init__.py │ │ ├── test_atom.py │ │ ├── test_base.py │ │ ├── test_bond.py │ │ ├── test_conformer.py │ │ └── test_mol.py │ ├── test_cross_validation │ │ ├── __init__.py │ │ └── test_similarity_threshold.py │ ├── test_data │ │ ├── __init__.py │ │ └── test_data.py │ ├── test_features │ │ ├── __init__.py │ │ ├── test_autocorrelation.py │ │ └── test_caching.py │ ├── test_featurizers.py │ ├── test_filters │ │ ├── __init__.py │ │ └── test_filters.py │ ├── test_io │ │ ├── __init__.py │ │ ├── test_sdf.py │ │ └── test_smiles.py │ └── test_standardizers │ │ ├── __init__.py │ │ └── test_chemaxon.py ├── utils │ ├── __init__.py │ ├── helpers.py │ ├── io.py │ ├── progress.py │ ├── string.py │ └── suppress.py └── vis │ ├── __init__.py │ ├── atom.py │ └── mol.py └── test_requirements.txt /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lewisacidic/scikit-chem/HEAD/.coveragerc -------------------------------------------------------------------------------- /.gitignore: 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