├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── ci.yml ├── .gitignore ├── CITATION.bib ├── LICENSE ├── README.md ├── data ├── README.md ├── combinatorial_library │ └── README.md ├── external │ ├── README.md │ └── pkidb_2025-04-15.sdf ├── filters │ ├── Brenk │ │ ├── README.md │ │ └── unwanted_substructures.csv │ ├── Enamine │ │ ├── Enamine_Building_Blocks.sdf │ │ ├── README.md │ │ └── most_similar_enamine_fragment.sdf │ ├── README.md │ └── retrosynthesizability │ │ ├── README.md │ │ └── retro.txt ├── fragment_library │ ├── AP.sdf │ ├── B1.sdf │ ├── B2.sdf │ ├── FP.sdf │ ├── GA.sdf │ ├── README.md │ ├── SE.sdf │ ├── X.sdf │ └── original_ligands.json ├── fragment_library_custom_filtered │ ├── AP.sdf │ ├── B1.sdf │ ├── B2.sdf │ ├── FP.sdf │ ├── GA.sdf │ ├── README.md │ ├── SE.sdf │ └── custom_filter_results.csv ├── fragment_library_filtered │ ├── AP.sdf │ ├── B1.sdf │ ├── B2.sdf │ ├── FP.sdf │ ├── GA.sdf │ ├── README.md │ └── SE.sdf ├── fragment_library_old │ └── README.md └── fragment_library_reduced │ ├── AP.sdf │ ├── B1.sdf │ ├── B2.sdf │ ├── FP.sdf │ ├── GA.sdf │ ├── README.md │ └── SE.sdf ├── docs ├── demos │ └── KinFragLib_demo.ipynb └── img │ └── toc_github_kinfraglib.png ├── environment.yml ├── kinfraglib ├── __init__.py ├── filters │ ├── __init__.py │ ├── analysis.py │ ├── brics_rules.py │ ├── check.py │ ├── drug_likeness.py │ ├── enamine_similar_fragments.py │ ├── enamine_substructures.py │ ├── pipeline.py │ ├── plots.py │ ├── prefilters.py │ ├── qed_threshold.ipynb │ ├── retro.py │ ├── synthesizability.py │ ├── unwanted_substructures.py │ └── utils.py └── utils.py ├── notebooks ├── README.md ├── custom_kinfraglib │ ├── 1_1_custom_filters_unwanted_substructures.ipynb │ ├── 1_2_custom_filters_drug_likeness.ipynb │ ├── 1_3_custom_filters_synthesizability.ipynb │ ├── 1_4_custom_filters_pairwise_retrosynthesizability.ipynb │ ├── 2_1_custom_filters_pipeline.ipynb │ ├── 2_2_custom_filters_analysis.ipynb │ ├── 2_3_custom_filters_kinase_mapping.ipynb │ ├── 2_4_custom_filters_paper.ipynb │ ├── README.md │ └── figures │ │ ├── kin_map_AP.png │ │ ├── n_fragments_filter_step.pdf │ │ ├── n_fragments_filter_total.pdf │ │ ├── n_fragments_per_subpocket.pdf │ │ ├── old_vs_new_kinfraglib.pdf │ │ ├── tsne_bool_bb.pdf │ │ ├── tsne_bool_brenk.pdf │ │ ├── tsne_bool_custom.pdf │ │ ├── tsne_bool_pains.pdf │ │ ├── tsne_bool_qed.pdf │ │ ├── tsne_bool_ro3.pdf │ │ ├── tsne_bool_syba.pdf │ │ └── tsne_original_ligands.pdf └── kinfraglib │ ├── 1_1_quick_start.ipynb │ ├── 2_1_fragment_analysis_original_ligands.ipynb │ ├── 2_2_fragment_analysis_statistics.ipynb │ ├── 2_3_fragment_analysis_most_common_fragments.ipynb │ ├── 2_4_highlight_fragments_in_ligand.ipynb │ ├── 3_1_fragment_library_reduced.ipynb │ ├── 4_1_combinatorial_library_data.ipynb │ ├── 4_2_combinatorial_library_properties.ipynb │ ├── 4_3_combinatorial_library_comparison_klifs.ipynb │ ├── 4_4_combinatorial_library_comparison_chembl.ipynb │ ├── 4_5_combinatorial_library_construct_ligands.ipynb │ ├── README.md │ └── figures │ ├── clustered_most_common_fragments_ap.svg │ ├── clustered_most_common_fragments_b1.svg │ ├── clustered_most_common_fragments_b2.svg │ ├── clustered_most_common_fragments_fp.svg │ ├── clustered_most_common_fragments_ga.svg │ ├── clustered_most_common_fragments_se.svg │ ├── combinatorial_library_active_kinase_targets.png │ ├── combinatorial_library_active_kinase_targets_activities.png │ ├── combinatorial_library_most_similar_chembl_molecules.pdf │ ├── combinatorial_library_ro5.pdf │ ├── descriptors.png │ ├── extreme_subpockets_one.png │ ├── extreme_subpockets_one_paper_b.png │ ├── extreme_subpockets_one_paper_c.png │ ├── extreme_subpockets_one_paper_d.png │ ├── extreme_subpockets_six_fragments.png │ ├── extreme_subpockets_six_ligand.png │ ├── fragments_3w2s_altA_chainA.png │ ├── highligh_fragments_in_ligand.png │ ├── inkscape_svg2png.sh │ ├── ligands_3w2s.png │ ├── n_fragments_per_subpocket.png │ ├── n_subpockets.png │ ├── similarities_by_kinase_group.png │ ├── 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