├── 1_Reading and Writing Smiles using rdKit.ipynb ├── 2_Property calculation, Drug-like filters, and Similarity maps.ipynb ├── 3_Fingerprint Generation and Similarity Analysis.ipynb ├── 4_Substructure and Similarity Search using rdKit.ipynb ├── README.md ├── data ├── 58_molobj.pkl ├── EGFR_compounds.csv ├── data_set.sdf ├── data_set.smi └── mps.csv ├── rdkit.yml └── retrosynth_models_comparison.ipynb /README.md: -------------------------------------------------------------------------------- 1 | 2 | **Installation and configuration:** 3 | 4 | Step 1: download and Install anaconda from anaconda.org 5 | 6 | Step 2: Install conda environment from rdkit.yml by using this command in anaconda terminal : "conda env create -f environment.yml" 7 | 8 | Step 3: check for installation : conda env list 9 | 10 | Step 4: Activate the environment : conda activate rdkit-training 11 | 12 | Step 5: check the list of packages available in rdkit-training env : conda list 13 | -------------------------------------------------------------------------------- /data/58_molobj.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suneelbvs/rdkit_tutorials/fda0f87390a1330fd7b32add169903581afe01a9/data/58_molobj.pkl -------------------------------------------------------------------------------- /data/data_set.sdf: -------------------------------------------------------------------------------- 1 | 2 | RDKit 2D 3 | 4 | 43 45 0 0 0 0 0 0 0 0999 V2000 5 | 1.3299 5.6152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -0.0967 5.1517 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7 | -0.4086 3.6844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -1.8351 3.2209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | -2.1470 1.7537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -1.0323 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | 0.7062 2.6807 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | 1.2760 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 14 | 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -1.0323 -0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 16 | 0.8578 -2.6401 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 17 | 2.3250 -2.9520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18 | -0.1459 -3.7548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19 | -1.1496 -4.8695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 20 | -2.6168 -4.5577 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 21 | -3.6205 -5.6724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 22 | -3.1570 -7.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 23 | -1.6897 -7.4108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 24 | -0.6860 -6.2961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 25 | 0.7812 -6.6080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 26 | -1.2262 -8.8374 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 27 | 0.2410 -9.1493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 28 | -4.1607 -8.2137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 29 | 2.7565 6.0787 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 30 | 0.8664 7.0418 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 31 | 1.7934 4.1886 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 32 | -2.9499 4.2246 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 33 | -3.5736 1.2902 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 34 | 2.1328 3.1443 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 35 | 2.7760 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 36 | -1.2606 -2.7511 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 37 | 0.8494 -4.4517 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 38 | -5.0877 -5.3605 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 39 | 2.2484 -6.9199 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 40 | 0.5216 -7.3617 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 41 | 1.1768 -5.4592 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 42 | 1.7082 -9.4612 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 43 | -0.0709 -10.6165 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 44 | 0.3105 -8.3552 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 45 | -5.1644 -9.3284 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 46 | -3.0459 -9.2174 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 47 | -5.2754 -7.2100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 48 | 1 2 1 0 49 | 2 3 1 0 50 | 3 4 2 0 51 | 4 5 1 0 52 | 5 6 2 0 53 | 6 7 1 0 54 | 7 8 2 0 55 | 7 9 1 0 56 | 9 10 1 0 57 | 10 11 2 0 58 | 10 12 1 0 59 | 12 13 2 0 60 | 12 14 1 1 61 | 14 15 1 0 62 | 15 16 2 0 63 | 16 17 1 0 64 | 17 18 2 0 65 | 18 19 1 0 66 | 19 20 2 0 67 | 20 21 1 0 68 | 19 22 1 0 69 | 22 23 1 0 70 | 18 24 1 0 71 | 8 3 1 0 72 | 20 15 1 0 73 | 11 6 1 0 74 | 1 25 1 0 75 | 1 26 1 0 76 | 1 27 1 0 77 | 4 28 1 0 78 | 5 29 1 0 79 | 8 30 1 0 80 | 9 31 1 0 81 | 14 32 1 0 82 | 14 33 1 0 83 | 17 34 1 0 84 | 21 35 1 0 85 | 21 36 1 0 86 | 21 37 1 0 87 | 23 38 1 0 88 | 23 39 1 0 89 | 23 40 1 0 90 | 24 41 1 0 91 | 24 42 1 0 92 | 24 43 1 0 93 | M END 94 | $$$$ 95 | -------------------------------------------------------------------------------- /data/data_set.smi: -------------------------------------------------------------------------------- 1 | SMILES Name 2 | [H]c1nc(C([H])([H])[S@](=O)c2nc3c([H])c([H])c(OC([H])([H])[H])c([H])c3n2[H])c(C([H])([H])[H])c(OC([H])([H])[H])c1C([H])([H])[H] 0 3 | -------------------------------------------------------------------------------- /data/mps.csv: 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Lett.";"2013";"" 31 | "CHEMBL2047959";"";"0";"500.63";"1";"2.93";"2";"COc1cc(ccc1Nc2nc(NC3CCCCC3)c4nc[nH]c4n2)N5CCN(CC5)S(=O)(=O)C";"IC50";"'='";"11";"nM";"7.96";"";"";"UO_0000065";"";"";"";"";"False";"CHEMBL3096273";"Cytotoxicity against human HCT116 cells";"F";"BAO_0000219";"cell-based format";"Homo sapiens";"";"";"HCT-116";"";"CHEMBL394";"HCT-116";"Homo sapiens";"CELL-LINE";"CHEMBL3091390";"1";"Scientific Literature";"Bioorg. Med. Chem. Lett.";"2013";"CHEMBL3308372" 32 | "CHEMBL3092036";"";"0";"433.56";"0";"4.96";"29";"COc1cc(ccc1Nc2ncc3cccc(NC4CCCCC4)c3n2)N5CCOCC5";"IC50";"'='";"9";"nM";"8.05";"";"";"UO_0000065";"18.56";"0.34";"3.09";"11.25";"False";"CHEMBL3096274";"Inhibition of full-length Mps1 kinase (unknown origin)";"B";"BAO_0000357";"single protein format";"Homo sapiens";"";"";"";"";"CHEMBL3983";"Dual specificity protein kinase TTK";"Homo sapiens";"SINGLE PROTEIN";"CHEMBL3091390";"1";"Scientific Literature";"Bioorg. Med. Chem. Lett.";"2013";"" 33 | "CHEMBL3092038";"";"0";"490.59";"0";"3.53";"31";"COc1cc(ccc1Nc2ncc3cccc(c4cccnc4)c3n2)N5CCN(CC5)S(=O)(=O)C";"IC50";"'='";"1580";"nM";"5.8";"";"";"UO_0000065";"";"";"";"";"False";"CHEMBL3096273";"Cytotoxicity against human HCT116 cells";"F";"BAO_0000219";"cell-based format";"Homo sapiens";"";"";"HCT-116";"";"CHEMBL394";"HCT-116";"Homo sapiens";"CELL-LINE";"CHEMBL3091390";"1";"Scientific Literature";"Bioorg. Med. Chem. Lett.";"2013";"CHEMBL3308372" 34 | -------------------------------------------------------------------------------- /rdkit.yml: -------------------------------------------------------------------------------- 1 | name: rdkit-training 2 | channels: 3 | - rdkit 4 | - defaults 5 | dependencies: 6 | - blas=1.0=mkl 7 | - cairo=1.16.0=h1c23506_3 8 | - certifi=2021.5.30=py36haa95532_0 9 | - expat=2.4.9=h6c2663c_0 10 | - fontconfig=2.14.1=hc0defaf_1 11 | - freetype=2.12.1=ha860e81_0 12 | - glib=2.69.1=h5dc1a3c_2 13 | - intel-openmp=2022.1.0=h59b6b97_3788 14 | - jpeg=9e=h2bbff1b_0 15 | - lerc=3.0=hd77b12b_0 16 | - libboost=1.67.0=hd9e427e_4 17 | - libdeflate=1.8=h2bbff1b_5 18 | - libffi=3.4.2=hd77b12b_6 19 | - libiconv=1.16=h2bbff1b_2 20 | - libpng=1.6.37=h2a8f88b_0 21 | - libtiff=4.5.0=h6c2663c_1 22 | - libxml2=2.9.14=h0ad7f3c_0 23 | - lz4-c=1.9.4=h2bbff1b_0 24 | - mkl=2020.2=256 25 | - mkl-service=2.3.0=py36h196d8e1_0 26 | - mkl_fft=1.3.0=py36h46781fe_0 27 | - mkl_random=1.1.1=py36h47e9c7a_0 28 | - numpy=1.19.2=py36hadc3359_0 29 | - numpy-base=1.19.2=py36ha3acd2a_0 30 | - olefile=0.46=py36_0 31 | - pandas=1.1.5=py36hd77b12b_0 32 | - pcre=8.45=hd77b12b_0 33 | - pillow=8.3.1=py36h4fa10fc_0 34 | - pip=21.2.2=py36haa95532_0 35 | - pixman=0.40.0=h2bbff1b_1 36 | - py-boost=1.67.0=py36h8300f20_4 37 | - python=3.6.13=h3758d61_0 38 | - python-dateutil=2.8.2=pyhd3eb1b0_0 39 | - pytz=2021.3=pyhd3eb1b0_0 40 | - rdkit=2020.09.1.0=py36h3d1ada6_1 41 | - setuptools=58.0.4=py36haa95532_0 42 | - six=1.16.0=pyhd3eb1b0_1 43 | - sqlite=3.40.1=h2bbff1b_0 44 | - tk=8.6.12=h2bbff1b_0 45 | - vc=14.2=h21ff451_1 46 | - vs2015_runtime=14.27.29016=h5e58377_2 47 | - wheel=0.37.1=pyhd3eb1b0_0 48 | - wincertstore=0.2=py36h7fe50ca_0 49 | - xz=5.2.10=h8cc25b3_1 50 | - zlib=1.2.13=h8cc25b3_0 51 | - zstd=1.5.2=h19a0ad4_0 52 | - pip: 53 | - argon2-cffi==21.3.0 54 | - argon2-cffi-bindings==21.2.0 55 | - async-generator==1.10 56 | - attrs==22.2.0 57 | - backcall==0.2.0 58 | - bleach==4.1.0 59 | - cffi==1.15.1 60 | - colorama==0.4.5 61 | - cycler==0.11.0 62 | - dataclasses==0.8 63 | - decorator==5.1.1 64 | - defusedxml==0.7.1 65 | - entrypoints==0.4 66 | - importlib-metadata==4.8.3 67 | - ipykernel==5.5.6 68 | - ipython==7.16.3 69 | - ipython-genutils==0.2.0 70 | - ipywidgets==7.7.3 71 | - jedi==0.17.2 72 | - jinja2==3.0.3 73 | - jsonschema==3.2.0 74 | - jupyter==1.0.0 75 | - jupyter-client==7.1.2 76 | - jupyter-console==6.4.3 77 | - jupyter-core==4.9.2 78 | - jupyterlab-pygments==0.1.2 79 | - jupyterlab-widgets==1.1.2 80 | - kiwisolver==1.3.1 81 | - markupsafe==2.0.1 82 | - matplotlib==3.3.4 83 | - mistune==0.8.4 84 | - nbclient==0.5.9 85 | - nbconvert==6.0.7 86 | - nbformat==5.1.3 87 | - nest-asyncio==1.5.6 88 | - notebook==6.4.10 89 | - packaging==21.3 90 | - pandocfilters==1.5.0 91 | - parso==0.7.1 92 | - pickleshare==0.7.5 93 | - prometheus-client==0.16.0 94 | - prompt-toolkit==3.0.36 95 | - pycparser==2.21 96 | - pygments==2.14.0 97 | - pyparsing==3.0.9 98 | - pyrsistent==0.18.0 99 | - pywin32==305 100 | - pywinpty==1.1.6 101 | - pyzmq==25.0.0 102 | - qtconsole==5.2.2 103 | - qtpy==2.0.1 104 | - scipy==1.5.4 105 | - seaborn==0.11.2 106 | - send2trash==1.8.0 107 | - terminado==0.12.1 108 | - testpath==0.6.0 109 | - tornado==6.1 110 | - traitlets==4.3.3 111 | - typing-extensions==4.1.1 112 | - wcwidth==0.2.6 113 | - webencodings==0.5.1 114 | - widgetsnbextension==3.6.2 115 | - zipp==3.6.0 116 | prefix: C:\Users\sunee\anaconda3\envs\rdkit-training 117 | --------------------------------------------------------------------------------