├── .DS_Store ├── .gitignore ├── LICENSE ├── README.asciidoc ├── ch00_cover.asciidoc ├── ch01_introduction.asciidoc ├── ch02_installation.asciidoc ├── ch03_python.asciidoc ├── ch04_database.asciidoc ├── ch05_rdkit.asciidoc ├── ch06_similarity.asciidoc ├── ch07_graph.asciidoc ├── ch08_visualization.asciidoc ├── ch09_qsar.asciidoc ├── ch10_deeplearning.asciidoc ├── ch11_dlqsar.asciidoc ├── ch12_generativemodels.asciidoc ├── ch13_beyond.asciidoc ├── images ├── by-nc-sa.png ├── ch02 │ └── anaconda01.png ├── ch04 │ ├── chembl01.png │ ├── chembl02.png │ ├── chembl03.png │ ├── chembl04.png │ ├── chembl05.png │ ├── chembl06.png │ ├── chembl07.png │ └── zinc01.png ├── ch05 │ ├── ch05_01.png │ ├── ch05_02.png │ ├── ch05_03.png │ ├── ch05_04.png │ ├── ch05_05.png │ ├── ch05_06.png │ ├── ch05_07.png │ └── ch05_08.png ├── ch06 │ ├── apx_rvx.png │ ├── apx_rvx_suf.png │ ├── cls01.png │ └── vs01.png ├── ch07 │ ├── chemviz2.png │ ├── mcs01.png │ ├── mcs02.png │ ├── mcs03.png │ ├── mcs04.png │ ├── mcs05.png │ ├── mmp01.png │ ├── mmp02.png │ ├── mmp03.png │ ├── mmp04.png │ ├── mms01.png │ └── scaffold.png ├── ch08 │ ├── pca01.png │ ├── pca02.png │ └── tsne01.png ├── ch10 │ ├── ch10_1.png │ ├── ch10_2.png │ └── ch10_3.png ├── ch11 │ ├── ch11_01.png │ └── ch11_nfp.png ├── jupyter.png ├── mishimasyk.png ├── python_for_ci.png └── souyakuchan.png ├── mkpdf.sh ├── notebooks ├── Chembl_FXa.txt ├── ch05_Sildenafil vs Vardenafil.ipynb ├── ch05_compounds.sdf ├── ch05_hetero_shuffle.ipynb ├── ch05_rdkit.ipynb ├── ch06_nov_hts.sdf ├── ch06_similarity.ipynb ├── ch07_MCS.ipynb ├── ch07_MMS.ipynb ├── ch08 │ ├── CHEMBL2380240.sdf │ ├── CHEMBL3098111.sdf │ ├── CHEMBL3112474.sdf │ ├── CHEMBL3351489.sdf │ ├── CHEMBL3352684.sdf │ ├── CHEMBL3526050.sdf │ ├── CHEMBL3739366.sdf │ ├── CHEMBL3739395.sdf │ ├── CHEMBL3769367.sdf │ └── CHEMBL3867477.sdf ├── ch08_compounds.txt ├── ch08_visualization.ipynb ├── ch09_compounds.txt ├── ch09_qsar.ipynb ├── ch11_simple_dnn.ipynb └── ch12_rnn.ipynb ├── pdf └── 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