├── .codecov.yml ├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── CI.yaml │ ├── CI_integration.yaml │ ├── GPU_CI_integration.yaml │ └── docker_deploy.yaml ├── .gitignore ├── .lgtm.yml ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools ├── README.md ├── conda-envs │ ├── openadmet-models-gpu.yaml │ └── openadmet-models.yaml ├── containers │ └── Dockerfile └── scripts │ └── create_conda_env.py ├── docs ├── Makefile ├── README.md ├── _api │ ├── api │ │ ├── active_learning │ │ │ ├── acquisition_functions.rst │ │ │ ├── committee.rst │ │ │ ├── ensemble_base.rst │ │ │ └── index.rst │ │ ├── anvil │ │ │ ├── anvil_workflow.rst │ │ │ ├── index.rst │ │ │ ├── specification.rst │ │ │ └── workflow_base.rst │ │ ├── comparison │ │ │ ├── compare_base.rst │ │ │ ├── index.rst │ │ │ └── posthoc.rst │ │ ├── featurization │ │ │ ├── GAT.rst │ │ │ ├── chemprop.rst │ │ │ ├── descriptors.rst │ │ │ ├── feature_base.rst │ │ │ ├── feature_combiner.rst │ │ │ ├── fingerprints.rst │ │ │ ├── index.rst │ │ │ └── mtenn.rst │ │ ├── index.rst │ │ ├── inference │ │ │ ├── index.rst │ │ │ └── predict.rst │ │ ├── model_architectures │ │ │ ├── GAT.rst │ │ │ ├── catboost.rst │ │ │ ├── chemprop.rst │ │ │ ├── dummy.rst │ │ │ ├── index.rst │ │ │ ├── lgbm.rst │ │ │ ├── model_base.rst │ │ │ ├── mtenn.rst │ │ │ ├── random_forest.rst │ │ │ ├── svm.rst │ │ │ ├── tabpfn.rst │ │ │ └── xgboost.rst │ │ ├── model_evaluation │ │ │ ├── binary.rst │ │ │ ├── classification.rst │ │ │ ├── cross_validation.rst │ │ │ ├── eval_base.rst │ │ │ ├── index.rst │ │ │ ├── regression.rst │ │ │ ├── uncertainty.rst │ │ │ └── utils.rst │ │ ├── splitting │ │ │ ├── data_driven.rst │ │ │ ├── index.rst │ │ │ └── sklearn.rst │ │ └── training │ │ │ ├── index.rst │ │ │ ├── lightning.rst │ │ │ ├── sklearn.rst │ │ │ └── training_base.rst │ ├── cli │ │ ├── anvil.rst │ │ ├── compare.rst │ │ ├── index.rst │ │ └── predict.rst │ └── index.rst ├── _static │ ├── README.md │ ├── custom.css │ └── images │ │ └── logos │ │ ├── favicon-32x32.png │ │ └── logo.png ├── _templates │ └── README.md ├── anvil_reference.rst ├── api.rst ├── conf.py ├── developer_guide.rst ├── docs │ └── autosummary │ │ ├── anvil.rst │ │ └── modules.rst ├── index.rst ├── installation.rst ├── make.bat ├── requirements.yaml └── user_guide.rst ├── openadmet ├── __init__.py └── models │ ├── __init__.py │ ├── active_learning │ ├── __init__.py │ ├── acquisition.py │ ├── committee.py │ └── ensemble_base.py │ ├── anvil │ ├── __init__.py │ ├── specification.py │ ├── workflow.py │ └── workflow_base.py │ ├── architecture │ ├── __init__.py │ ├── catboost.py │ ├── chemprop.py │ ├── dummy.py │ ├── gat.py │ ├── lgbm.py │ ├── model_base.py │ ├── mtenn.py │ ├── nepare.py │ ├── rf.py │ ├── sklearn_pipeline.py │ ├── svm.py │ ├── tabpfn.py │ └── xgboost.py │ ├── cli │ ├── anvil.py │ ├── cli.py │ ├── compare.py │ └── predict.py │ ├── comparison │ ├── __init__.py │ ├── compare_base.py │ └── posthoc.py │ ├── drivers.py │ ├── eval │ ├── __init__.py │ ├── binary.py │ ├── classification.py │ ├── cross_validation.py │ ├── eval_base.py │ ├── regression.py │ ├── uncertainty.py │ └── utils.py │ ├── features │ ├── __init__.py │ ├── chemprop.py │ ├── combine.py │ ├── feature_base.py │ ├── gat_featurizer.py │ ├── molfeat_fingerprint.py │ ├── molfeat_properties.py │ ├── mtenn.py │ └── pairwise.py │ ├── inference │ ├── __init__.py │ └── inference.py │ ├── log.py │ ├── py.typed │ ├── registries.py │ ├── split │ ├── __init__.py │ ├── cluster.py │ ├── scaffold.py │ ├── sklearn.py │ └── split_base.py │ ├── tests │ ├── __init__.py │ ├── integration │ │ ├── README.md │ │ ├── datafiles.py │ │ ├── test_anvil_integration.py │ │ └── test_data │ │ │ ├── catboost_prop_dissimilarity.yaml │ │ │ ├── chemeleon_MT.yaml │ │ │ ├── chemeleon_MT_ensemble.yaml │ │ │ ├── chemprop_AChE_finetune.yaml │ │ │ ├── chemprop_AChE_finetune_ensemble.yaml │ │ │ ├── chemprop_MT.yaml │ │ │ ├── chemprop_MT_cpu_single.yaml │ │ │ ├── chemprop_MT_cpu_single_train_test.yaml │ │ │ ├── chemprop_ST.yaml │ │ │ ├── cross_validation_metrics_combined.json │ │ │ ├── cross_validation_metrics_descr.json │ │ │ ├── cross_validation_metrics_fp.json │ │ │ ├── cyp_multitask.csv │ │ │ ├── cyp_multitask_nepare.csv │ │ │ ├── cyp_multitask_test.csv │ │ │ ├── cyp_multitask_train.csv │ │ │ ├── cyp_multitask_val.csv │ │ │ ├── dummy_fp.yaml │ │ │ ├── lgbm_fp_cv.yaml │ │ │ ├── lgbm_fp_cv_train_test.yaml │ │ │ ├── lgbm_fp_ensemble.yaml │ │ │ ├── lgbm_fp_prop_gridsearch_cv.yaml │ │ │ ├── lgbm_mordred_cv_impute.yaml │ │ │ ├── lgbm_prop_scaffold_cv.yaml │ │ │ ├── mtenn_anvil.yaml │ │ │ ├── nepare_fp.yaml │ │ │ ├── pose_data │ │ │ └── cyp3a4_processed_poses │ │ │ │ ├── 3nxu_processed_aligned_final_renamed.pdb │ │ │ │ ├── 3tjs_processed_aligned_final_renamed.pdb │ │ │ │ ├── 3ua1_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4i4g_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4i4h_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4k9t_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4k9u_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4k9v_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4k9w_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4k9x_processed_aligned_final_renamed.pdb │ │ │ │ ├── 4ny4_processed_aligned_final_renamed.pdb │ │ │ │ ├── 5te8_processed_aligned_final_renamed.pdb │ │ │ │ ├── 5vc0_processed_aligned_final_renamed.pdb │ │ │ │ ├── 5vce_processed_aligned_final_renamed.pdb │ │ │ │ ├── 5vcg_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bcz_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bd5_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bd6_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bd7_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bd8_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bdh_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bdi_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bdk_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6bdm_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6da2_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6da3_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6da5_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6da8_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6daa_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6dab_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6dac_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6dag_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6daj_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6dal_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6ma6_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6ma7_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6ma8_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6oo9_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6ooa_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6oob_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6une_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6ung_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6unh_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6uni_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6unj_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6unk_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6unl_processed_aligned_final_renamed.pdb │ │ │ │ ├── 6unm_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ks8_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ksa_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvh_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvi_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvj_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvk_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvm_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvn_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvo_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvp_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvq_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7kvs_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7lxl_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7uay_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7uaz_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7uf9_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ufa_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ufb_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ufc_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ufd_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7ufe_processed_aligned_final_renamed.pdb │ │ │ │ ├── 7uff_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8dyc_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewd_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewe_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewl_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewm_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewn_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewp_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewq_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ewr_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8ews_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8exb_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8so1_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8so2_processed_aligned_final_renamed.pdb │ │ │ │ ├── 8spd_processed_aligned_final_renamed.pdb │ │ │ │ ├── ray.png │ │ │ │ └── test.png │ │ │ ├── poses.csv │ │ │ ├── rf_scaffold_cv.yaml │ │ │ ├── tabpfn.yaml │ │ │ └── xgboost_prop_perimeter_cv.yaml │ ├── test_utils.py │ └── unit │ │ ├── __init__.py │ │ ├── active_learning │ │ ├── __init__.py │ │ └── test_active_learning.py │ │ ├── anvil │ │ ├── __init__.py │ │ └── test_anvil.py │ │ ├── cli │ │ └── test_cli.py │ │ ├── comparison │ │ └── test_comparison.py │ │ ├── data │ │ ├── __init__.py │ │ └── test_data.py │ │ ├── datafiles.py │ │ ├── eval │ │ ├── __init__.py │ │ └── test_eval.py │ │ ├── features │ │ ├── __init__.py │ │ ├── test_features.py │ │ ├── test_mtenn.py │ │ └── test_nepare.py │ │ ├── inference │ │ ├── __init__.py │ │ └── test_inference.py │ │ ├── models │ │ ├── __init__.py │ │ ├── test_base.py │ │ ├── test_lgbm.py │ │ └── test_nepare.py │ │ ├── split │ │ ├── __init__.py │ │ └── test_splitters.py │ │ ├── test_data │ │ ├── 7kvh_A.pdb │ │ ├── ACEH_chembl_pchembl.csv │ │ ├── AChE_CHEMBL4078_Landrum_maxcur.csv │ │ ├── CYP3A4_chembl_pchembl.csv │ │ ├── PXR_tox21_withNan.parquet │ │ ├── __init__.py │ │ ├── aceh_chemprop_anvil_model_dir │ │ │ ├── anvil_recipe.yaml │ │ │ ├── checkpoints │ │ │ │ ├── best-epoch=9-train_loss=0.3325.ckpt │ │ │ │ └── last.ckpt │ │ │ ├── logs │ │ │ │ └── model │ │ │ │ │ └── version_0 │ │ │ │ │ ├── hparams.yaml │ │ │ │ │ └── metrics.csv │ │ │ ├── model.json │ │ │ ├── model.pth │ │ │ ├── recipe_components │ │ │ │ ├── data.yaml │ │ │ │ ├── eval.yaml │ │ │ │ ├── metadata.yaml │ │ │ │ └── procedure.yaml │ │ │ ├── regplot.png │ │ │ ├── regression_metrics.json │ │ │ ├── test_dataloader.pth │ │ │ └── train_dataloader.pth │ │ ├── acetylcholinesterase_anvil_chemprop.yaml │ │ ├── anvil_featconcat.yaml │ │ ├── anvil_gridsearch.yaml │ │ ├── anvil_xgbm_cv_1_1.yaml │ │ ├── basic_anvil.yaml │ │ ├── basic_anvil_classification.yaml │ │ ├── basic_anvil_cv.yaml │ │ ├── basic_anvil_data.yaml │ │ ├── basic_anvil_eval.yaml │ │ ├── basic_anvil_gat.yaml │ │ ├── basic_anvil_metadata.yaml │ │ ├── basic_anvil_procedure.yaml │ │ ├── cross_validation_metrics_1a2.json │ │ ├── cross_validation_metrics_2c9.json │ │ ├── cross_validation_metrics_3a4.json │ │ ├── cross_validation_metrics_multitask.json │ │ ├── cyp3a4_anvil_lgbm_model_dir │ │ │ ├── anvil_recipe.yaml │ │ │ ├── cross_validation_metrics.json │ │ │ ├── cross_validation_regplot.png │ │ │ ├── model.json │ │ │ ├── model.pkl │ │ │ ├── recipe_components │ │ │ │ ├── data.yaml │ │ │ │ ├── eval.yaml │ │ │ │ ├── metadata.yaml │ │ │ │ └── procedure.yaml │ │ │ ├── regplot.png │ │ │ └── regression_metrics.json │ │ ├── example_intake.yaml │ │ ├── ligands.csv │ │ ├── make_intake_cat.ipynb │ │ ├── tabpfn_ache.yaml │ │ └── test_data.csv │ │ └── test_utils.py │ ├── trainer │ ├── lightning.py │ 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