├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── 00_bug_report.md │ ├── 10_feature_request.md │ └── 20_help_request.md ├── PUll_REQUEST_TEMPLATE │ └── pull_request_template.md ├── dependabot.yml └── workflows │ ├── build.yml │ └── cffconvert.yml ├── .gitignore ├── .prospector.yml ├── .readthedocs.yml ├── .zenodo.json ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.rst ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.rst ├── data ├── Amines │ └── CDFT │ │ ├── all_amines.csv │ │ └── all_geometries_amines.json ├── Carboxylic_acids │ ├── CDFT │ │ ├── all_carboxylics.csv │ │ ├── all_geometries_carboxylics.json │ │ ├── cdft_random_500.csv │ │ └── training │ │ │ ├── All_models_11k.json │ │ │ ├── All_models_1k.json │ │ │ ├── All_models_2k.json │ │ │ ├── All_models_500.json │ │ │ ├── All_models_5k.json │ │ │ └── All_models_7k.json │ ├── GDB13 │ │ ├── Results │ │ │ ├── Activity_coefficients_Toluene │ │ │ │ └── data.tgz │ │ │ ├── Filter │ │ │ │ └── gdb13_carboxylic_acid_candidates.csv │ │ │ └── ligand_database.zip │ │ └── eMolecules_COO.gz │ └── input_settings_cdft1.yaml ├── ResulsTraining.md └── Training_hyperparameters.md ├── docs ├── Makefile ├── _static │ └── theme_overrides.css ├── _templates │ └── .gitignore ├── api_data.rst ├── api_models.rst ├── available_models.rst ├── conf.py ├── includereadme.rst ├── index.rst ├── make.bat ├── training_and_validation.rst └── tutorial_models.rst ├── notebooks └── Filter_visualization.ipynb ├── scripts ├── predict_all.py ├── predict_gp.py ├── predict_torch.py ├── run_gp_models.py ├── run_scikit_models.py ├── run_torch_models.py ├── search_scikit_hyper.py └── utils │ ├── extract_cdft_properties.py │ ├── extract_geometries.py │ ├── extract_results.py │ ├── plot_rvalues.py │ ├── remove_duplicates.py │ └── remove_non_organic.py ├── setup.cfg ├── setup.py ├── swan ├── __init__.py ├── __version__.py ├── dataset │ ├── __init__.py │ ├── data_graph_base.py │ ├── dgl_graph_data.py │ ├── features │ │ ├── __init__.py │ │ ├── atomic_features.py │ │ └── featurizer.py │ ├── fingerprints_data.py │ ├── geometry.py │ ├── graph │ │ └── molecular_graph.py │ ├── sanitize_data.py │ ├── splitter.py │ ├── swan_data_base.py │ └── torch_geometric_graph_data.py ├── modeller │ ├── __init__.py │ ├── base_modeller.py │ ├── gp_modeller.py │ ├── models │ │ ├── __init__.py │ │ ├── equivariant_models.py │ │ ├── fingerprint_models.py │ │ ├── gaussian_process.py │ │ ├── graph_models.py │ │ └── se3_transformer.py │ ├── scikit_modeller.py │ └── torch_modeller.py ├── state │ ├── __init__.py │ └── state.py ├── type_hints.py └── utils │ ├── __init__.py │ ├── early_stopping.py │ ├── log_config.py │ └── plot.py └── tests ├── __init__.py ├── files ├── cdft_geometries.json ├── cdft_properties.csv ├── fingerprint_swan_models.pt ├── fingerprint_swan_scales.pkl ├── graph_swan_models.pt ├── graph_swan_scales.pkl ├── input_test_e3nn_train.yml ├── input_test_fingerprint_predict.yml ├── input_test_fingerprint_train.yml ├── input_test_graph_geometries.yml ├── input_test_graph_predict.yml ├── input_test_graph_train.yml ├── mypy.ini ├── smiles.csv └── thousand.csv ├── test_dataset.py ├── test_e3nn.py ├── test_featurizer.py ├── test_fingerprint_modeller.py ├── test_gpytorch.py ├── test_mpnn.py ├── test_mypy.py ├── test_plot.py ├── test_scikit_models.py ├── test_se3_transformer.py ├── test_sphinx.py ├── test_state.py └── utils_test.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.editorconfig -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/00_bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/ISSUE_TEMPLATE/00_bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/10_feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/ISSUE_TEMPLATE/10_feature_request.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/20_help_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/ISSUE_TEMPLATE/20_help_request.md -------------------------------------------------------------------------------- /.github/PUll_REQUEST_TEMPLATE/pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/PUll_REQUEST_TEMPLATE/pull_request_template.md -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/build.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/workflows/build.yml -------------------------------------------------------------------------------- /.github/workflows/cffconvert.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.github/workflows/cffconvert.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.gitignore -------------------------------------------------------------------------------- /.prospector.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.prospector.yml -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.readthedocs.yml -------------------------------------------------------------------------------- /.zenodo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/.zenodo.json -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/CITATION.cff -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/CODE_OF_CONDUCT.rst -------------------------------------------------------------------------------- /CONTRIBUTING.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/CONTRIBUTING.rst -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /NOTICE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/NOTICE -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/README.rst -------------------------------------------------------------------------------- /data/Amines/CDFT/all_amines.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Amines/CDFT/all_amines.csv -------------------------------------------------------------------------------- /data/Amines/CDFT/all_geometries_amines.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Amines/CDFT/all_geometries_amines.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/all_carboxylics.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/all_carboxylics.csv -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/all_geometries_carboxylics.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/all_geometries_carboxylics.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/cdft_random_500.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/cdft_random_500.csv -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/training/All_models_11k.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/training/All_models_11k.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/training/All_models_1k.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/training/All_models_1k.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/training/All_models_2k.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/training/All_models_2k.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/training/All_models_500.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/training/All_models_500.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/training/All_models_5k.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/training/All_models_5k.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/CDFT/training/All_models_7k.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/CDFT/training/All_models_7k.json -------------------------------------------------------------------------------- /data/Carboxylic_acids/GDB13/Results/Activity_coefficients_Toluene/data.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/GDB13/Results/Activity_coefficients_Toluene/data.tgz -------------------------------------------------------------------------------- /data/Carboxylic_acids/GDB13/Results/Filter/gdb13_carboxylic_acid_candidates.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/GDB13/Results/Filter/gdb13_carboxylic_acid_candidates.csv -------------------------------------------------------------------------------- /data/Carboxylic_acids/GDB13/Results/ligand_database.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/GDB13/Results/ligand_database.zip -------------------------------------------------------------------------------- /data/Carboxylic_acids/GDB13/eMolecules_COO.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/GDB13/eMolecules_COO.gz -------------------------------------------------------------------------------- /data/Carboxylic_acids/input_settings_cdft1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Carboxylic_acids/input_settings_cdft1.yaml -------------------------------------------------------------------------------- /data/ResulsTraining.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/ResulsTraining.md -------------------------------------------------------------------------------- /data/Training_hyperparameters.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/data/Training_hyperparameters.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_static/theme_overrides.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/_static/theme_overrides.css -------------------------------------------------------------------------------- /docs/_templates/.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/api_data.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/api_data.rst -------------------------------------------------------------------------------- /docs/api_models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/api_models.rst -------------------------------------------------------------------------------- /docs/available_models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/available_models.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/includereadme.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../README.rst 2 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/training_and_validation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/training_and_validation.rst -------------------------------------------------------------------------------- /docs/tutorial_models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/docs/tutorial_models.rst -------------------------------------------------------------------------------- /notebooks/Filter_visualization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/notebooks/Filter_visualization.ipynb -------------------------------------------------------------------------------- /scripts/predict_all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/predict_all.py -------------------------------------------------------------------------------- /scripts/predict_gp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/predict_gp.py -------------------------------------------------------------------------------- /scripts/predict_torch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/predict_torch.py -------------------------------------------------------------------------------- /scripts/run_gp_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/run_gp_models.py -------------------------------------------------------------------------------- /scripts/run_scikit_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/run_scikit_models.py -------------------------------------------------------------------------------- /scripts/run_torch_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/run_torch_models.py -------------------------------------------------------------------------------- /scripts/search_scikit_hyper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/search_scikit_hyper.py -------------------------------------------------------------------------------- /scripts/utils/extract_cdft_properties.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/utils/extract_cdft_properties.py -------------------------------------------------------------------------------- /scripts/utils/extract_geometries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/utils/extract_geometries.py -------------------------------------------------------------------------------- /scripts/utils/extract_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/utils/extract_results.py -------------------------------------------------------------------------------- /scripts/utils/plot_rvalues.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/utils/plot_rvalues.py -------------------------------------------------------------------------------- /scripts/utils/remove_duplicates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/utils/remove_duplicates.py -------------------------------------------------------------------------------- /scripts/utils/remove_non_organic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/scripts/utils/remove_non_organic.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/setup.py -------------------------------------------------------------------------------- /swan/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/__init__.py -------------------------------------------------------------------------------- /swan/__version__.py: -------------------------------------------------------------------------------- 1 | __version__ = '0.7.0' 2 | -------------------------------------------------------------------------------- /swan/dataset/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/__init__.py -------------------------------------------------------------------------------- /swan/dataset/data_graph_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/data_graph_base.py -------------------------------------------------------------------------------- /swan/dataset/dgl_graph_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/dgl_graph_data.py -------------------------------------------------------------------------------- /swan/dataset/features/__init__.py: -------------------------------------------------------------------------------- 1 | """Features API.""" -------------------------------------------------------------------------------- /swan/dataset/features/atomic_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/features/atomic_features.py -------------------------------------------------------------------------------- /swan/dataset/features/featurizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/features/featurizer.py -------------------------------------------------------------------------------- /swan/dataset/fingerprints_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/fingerprints_data.py -------------------------------------------------------------------------------- /swan/dataset/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/geometry.py -------------------------------------------------------------------------------- /swan/dataset/graph/molecular_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/graph/molecular_graph.py -------------------------------------------------------------------------------- /swan/dataset/sanitize_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/sanitize_data.py -------------------------------------------------------------------------------- /swan/dataset/splitter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/splitter.py -------------------------------------------------------------------------------- /swan/dataset/swan_data_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/swan_data_base.py -------------------------------------------------------------------------------- /swan/dataset/torch_geometric_graph_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/dataset/torch_geometric_graph_data.py -------------------------------------------------------------------------------- /swan/modeller/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/__init__.py -------------------------------------------------------------------------------- /swan/modeller/base_modeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/base_modeller.py -------------------------------------------------------------------------------- /swan/modeller/gp_modeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/gp_modeller.py -------------------------------------------------------------------------------- /swan/modeller/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/models/__init__.py -------------------------------------------------------------------------------- /swan/modeller/models/equivariant_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/models/equivariant_models.py -------------------------------------------------------------------------------- /swan/modeller/models/fingerprint_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/models/fingerprint_models.py -------------------------------------------------------------------------------- /swan/modeller/models/gaussian_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/models/gaussian_process.py -------------------------------------------------------------------------------- /swan/modeller/models/graph_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/models/graph_models.py -------------------------------------------------------------------------------- /swan/modeller/models/se3_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/models/se3_transformer.py -------------------------------------------------------------------------------- /swan/modeller/scikit_modeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/scikit_modeller.py -------------------------------------------------------------------------------- /swan/modeller/torch_modeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/modeller/torch_modeller.py -------------------------------------------------------------------------------- /swan/state/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/state/__init__.py -------------------------------------------------------------------------------- /swan/state/state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/state/state.py -------------------------------------------------------------------------------- /swan/type_hints.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/type_hints.py -------------------------------------------------------------------------------- /swan/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /swan/utils/early_stopping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/utils/early_stopping.py -------------------------------------------------------------------------------- /swan/utils/log_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/utils/log_config.py -------------------------------------------------------------------------------- /swan/utils/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/swan/utils/plot.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | -------------------------------------------------------------------------------- /tests/files/cdft_geometries.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/cdft_geometries.json -------------------------------------------------------------------------------- /tests/files/cdft_properties.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/cdft_properties.csv -------------------------------------------------------------------------------- /tests/files/fingerprint_swan_models.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/fingerprint_swan_models.pt -------------------------------------------------------------------------------- /tests/files/fingerprint_swan_scales.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/fingerprint_swan_scales.pkl -------------------------------------------------------------------------------- /tests/files/graph_swan_models.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/graph_swan_models.pt -------------------------------------------------------------------------------- /tests/files/graph_swan_scales.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/graph_swan_scales.pkl -------------------------------------------------------------------------------- /tests/files/input_test_e3nn_train.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/input_test_e3nn_train.yml -------------------------------------------------------------------------------- /tests/files/input_test_fingerprint_predict.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/input_test_fingerprint_predict.yml -------------------------------------------------------------------------------- /tests/files/input_test_fingerprint_train.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/input_test_fingerprint_train.yml -------------------------------------------------------------------------------- /tests/files/input_test_graph_geometries.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/input_test_graph_geometries.yml -------------------------------------------------------------------------------- /tests/files/input_test_graph_predict.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/input_test_graph_predict.yml -------------------------------------------------------------------------------- /tests/files/input_test_graph_train.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/input_test_graph_train.yml -------------------------------------------------------------------------------- /tests/files/mypy.ini: -------------------------------------------------------------------------------- 1 | [mypy] 2 | ignore_missing_imports = True -------------------------------------------------------------------------------- /tests/files/smiles.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/smiles.csv -------------------------------------------------------------------------------- /tests/files/thousand.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/files/thousand.csv -------------------------------------------------------------------------------- /tests/test_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_dataset.py -------------------------------------------------------------------------------- /tests/test_e3nn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_e3nn.py -------------------------------------------------------------------------------- /tests/test_featurizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_featurizer.py -------------------------------------------------------------------------------- /tests/test_fingerprint_modeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_fingerprint_modeller.py -------------------------------------------------------------------------------- /tests/test_gpytorch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_gpytorch.py -------------------------------------------------------------------------------- /tests/test_mpnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_mpnn.py -------------------------------------------------------------------------------- /tests/test_mypy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_mypy.py -------------------------------------------------------------------------------- /tests/test_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_plot.py -------------------------------------------------------------------------------- /tests/test_scikit_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_scikit_models.py -------------------------------------------------------------------------------- /tests/test_se3_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_se3_transformer.py -------------------------------------------------------------------------------- /tests/test_sphinx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_sphinx.py -------------------------------------------------------------------------------- /tests/test_state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/test_state.py -------------------------------------------------------------------------------- /tests/utils_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlesc-nano/swan/HEAD/tests/utils_test.py --------------------------------------------------------------------------------