├── .github └── workflows │ ├── CI.yml │ ├── docs.yml │ └── nice.yml ├── .gitignore ├── CHANGELOG ├── CITATION.cff ├── LICENSE-3RD-PARTY.txt ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs ├── acknowledgments.md ├── api │ ├── al.md │ ├── chemspace.md │ └── rmol.md ├── environment.yml ├── index.md ├── installation.md ├── license.md ├── notebooks │ ├── notebook1-basic-tutorial-full │ │ ├── 1_basic_tutorial_full.md │ │ ├── output_11_0.png │ │ ├── output_14_0.png │ │ ├── output_15_0.jpg │ │ ├── output_15_0.png │ │ ├── output_27_1.png │ │ ├── output_6_0.jpg │ │ └── output_6_0.png │ ├── notebook2-mini-tutorial-grow-linker-and-r-group │ │ ├── 2_mini_tutorial_grow_linker_rgroup.md │ │ ├── output_10_0.png │ │ ├── output_11_0.png │ │ ├── output_14_0.png │ │ ├── output_15_0.png │ │ ├── output_17_0.png │ │ ├── output_4_0.jpg │ │ ├── output_4_0.png │ │ ├── output_6_0.jpg │ │ └── output_6_0.png │ ├── notebook2.1-tutorial-single-molecule │ │ ├── 2_tutorial_single_mol.md │ │ ├── output_15_0.png │ │ ├── output_16_0.jpg │ │ ├── output_16_0.png │ │ ├── output_17_0.png │ │ ├── output_24_0.png │ │ ├── output_25_0.png │ │ ├── output_27_0.jpg │ │ ├── output_27_0.png │ │ ├── output_39_1.png │ │ ├── output_9_0.jpg │ │ └── output_9_0.png │ ├── notebook3-mini-tutorial-replace-substructure │ │ ├── 3_mini_tutorial_replace_substructure.md │ │ ├── output_10_0.png │ │ ├── output_4_0.jpg │ │ ├── output_4_0.png │ │ ├── output_6_0.jpg │ │ └── output_6_0.png │ ├── notebook4-introduce-chemspace │ │ ├── 4_tutorial_introduce_chemspace.md │ │ ├── output_27_0.jpg │ │ ├── output_27_0.png │ │ ├── output_9_0.jpg │ │ └── output_9_0.png │ ├── notebook5-chemspace-streamlined │ │ ├── 5_tutorial_chemspace_streamlined.md │ │ ├── output_6_0.jpg │ │ └── output_6_0.png │ ├── notebook6-chemspace-smiles │ │ └── 6_chemspace_smiles.md │ ├── notebook7-al-enamine │ │ └── 7_active_learning_enamine.md │ ├── notebook8-more-al │ │ └── 8_active_learning_details.md │ └── notebook9-previous-study50k │ │ └── 9_cs50k_study.md ├── references.bib ├── scripts │ └── gen_ref_pages.py └── tutorials │ ├── 0_basic │ ├── 0_basic_tutorial_full.md │ ├── output_11_0.png │ ├── output_14_0.png │ ├── output_15_0.jpg │ ├── output_15_0.png │ ├── output_27_1.png │ ├── output_6_0.jpg │ └── output_6_0.png │ ├── 1_chemspace │ ├── 1_tutorial_introduce_chemspace.md │ ├── output_27_0.jpg │ ├── output_27_0.png │ ├── output_9_0.jpg │ └── output_9_0.png │ └── 2_active_learning │ ├── 2_tutorial_active_learning.md │ ├── output_14_0.jpg │ ├── output_14_0.png │ ├── output_7_0.jpg │ └── output_7_0.png ├── environment.yml ├── fegrow ├── __init__.py ├── al.py ├── builder.py ├── cli │ ├── __init__.py │ ├── cli.py │ ├── scoring.py │ └── utils.py ├── conformers.py ├── data │ ├── fpscores.pkl.gz │ ├── linkers │ │ ├── library.sdf │ │ └── smiles.txt │ ├── rgroups │ │ ├── library.sdf │ │ └── reorder.py │ └── unwanted_substructures.csv ├── package.py ├── receptor.py ├── sascorer.py ├── testing │ ├── __init__.py │ ├── asapsmiles │ │ ├── asapsmiles.py │ │ ├── core.sdf │ │ ├── rec_final.pdb │ │ └── sars_generated_smiles.txt │ ├── conftest.py │ ├── data │ │ ├── 5R83_core.sdf │ │ ├── 5R83_rec.pdb │ │ ├── 7L10_final.pdb │ │ ├── co.mol │ │ ├── cs50k_scored49578_unique47710.csv.zip │ │ ├── ethanol.mol │ │ ├── sarcov2_coreh_cut.sdf │ │ └── sarscov2_coreh.sdf │ ├── library_gen.py │ ├── run_al.py │ ├── test_chemspace.py │ ├── test_general.py │ └── test_receptor.py ├── toxicity.py └── version.txt ├── mkdocs.yml ├── notebooks ├── .tutorial.py ├── 10_chemspace_dask.ipynb ├── 1_basic_tutorial_full.ipynb ├── 2_mini_tutorial_grow_linker_rgroup.ipynb ├── 2_tutorial_single_mol.ipynb ├── 3_mini_tutorial_replace_substructure.ipynb ├── 4_tutorial_introduce_chemspace.ipynb ├── 5_tutorial_chemspace_streamlined.ipynb ├── 6_chemspace_smiles.ipynb ├── 7_active_learning_enamine.ipynb ├── 8_active_learning_details.ipynb ├── 9_cs50k_study.ipynb ├── linker_example │ ├── core.sdf │ ├── peplites-fl33.ipynb │ └── rec.pdb ├── manual_rgroups │ ├── 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