{"id":46413,"date":"2023-12-29T22:53:40","date_gmt":"2023-02-05T18:14:41","guid":{"rendered":"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/"},"modified":"2024-05-04T15:56:07","modified_gmt":"2024-05-04T07:56:07","slug":"46413-2","status":"publish","type":"post","link":"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/","title":{"rendered":""},"content":{"rendered":"

\u6982\u8981<\/h1>\n

chemoinfomatics\u3067\u4f7f\u308f\u308c\u308bpython\u306emodule\u306eRDKit\u3092jupyter-notebook\u3067\u4f7f\u3046\u969b\u3001\u74b0\u5883\u69cb\u7bc9\u306b\u3066\u3053\u3065\u3063\u305f\u306e\u3067\u3053\u3053\u306b\u66f8\u304d\u8a18\u3057\u307e\u3059\u3002<\/p>\n

\u74b0\u5883<\/h1>\n

macOS Mojave version 10.12.2<\/p>\n

RDKit\u3092\u4f7f\u3046\u4eee\u60f3\u74b0\u5883\u3092\u69cb\u7bc9<\/h1>\n

RDKit\u306e\u516c\u5f0f\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8\u306b\u6cbf\u3063\u3066\u3001RDKit\u3092\u4f7f\u3048\u308b\u4eee\u60f3\u74b0\u5883\u3092conda\u30b3\u30de\u30f3\u30c9\u3067\u4f5c\u6210\u3002<\/p>\n

conda create -c rdkit -n my-rdkit-env rdkit # my-rdkit-env \u306f\u4efb\u610f\u306e\u74b0\u5883\u540d\r\n<\/code><\/pre>\n
\u3057\u3070\u3089\u304f\u3059\u308b\u3068<\/p>\n
Proceed ([y]\/n)?\r\n<\/code><\/pre>\n
\u3068\u805e\u304b\u308c\u308b\u306e\u3067y\u3067\u7d9a\u884c\u3002\u5404\u7a2emodule\u306einstall\u304c\u59cb\u307e\u308a\u307e\u3059\u3002install\u7d42\u4e86\u5f8c<\/p>\n
conda activate my-rdkit-env\r\n<\/code><\/pre>\n
\u3068\u5165\u529b\u3002terminal\u306e\u884c\u306e\u5de6\u306b(my-rdkit-env)\u3068\u51fa\u3066\u3044\u308b\u306f\u305a\u3067\u3059\u3002\u3053\u308c\u306fmy-rdkit_env\u3068\u3044\u3044\u4eee\u60f3\u74b0\u5883\u306b\u5165\u3063\u3066\u3044\u308b\u3053\u3068\u3092\u8868\u3057\u307e\u3059\u3002conda deactivate\u3067\u4eee\u60f3\u74b0\u5883\u304b\u3089\u51fa\u3089\u308c\u307e\u3059\u3002<\/p>\n
\u3053\u3053\u3067\u3053\u306e\u4eee\u60f3\u74b0\u5883\u306b\u5fc5\u8981\u306amodule\u3092install\u3057\u307e\u3059\u3002
\n\u3053\u3053\u3067\u306frdkit\u3068\u4e00\u7dd2\u306b\u3088\u304f\u4f7f\u308f\u308c\u308bpubchempy\u3092install\u3057\u307e\u3059\u3002<\/p>\n
pip install pubchempy\r\n<\/code><\/pre>\n
python3\u3068\u5165\u529b\u3057\u3001python console\u306b\u5165\u308a\u307e\u3059\u3002<\/p>\n
>>> from rdkit import Chem\r\n>>> Chem.MolFromSmiles('C1=CC=CC=C1') # 'C1=CC=CC=C1'\u306fbenzene\u306esmiles\u8868\u8a18\r\n<rdkit.Chem.rdchem.Mol object at 0x109bc6030>\r\n<\/code><\/pre>\n
\u3068\u306a\u308c\u3070\u3068\u308a\u3042\u3048\u305a\u4eee\u60f3\u74b0\u5883\u69cb\u7bc9\u5b8c\u4e86\u3067\u3059\u3002<\/p>\n
jupyter-notebook\u3067\u4eee\u60f3\u74b0\u5883\u3092\u4f7f\u7528<\/h1>\n
\u3053\u3061\u3089\u306e\u8a18\u4e8b\u304c\u975e\u5e38\u306b\u308f\u304b\u308a\u3084\u3059\u304f\u307e\u3068\u3081\u3066\u304f\u3060\u3055\u3063\u3066\u3044\u308b\u306e\u3067\u53c2\u8003\u306b\u3057\u307e\u3059\u3002<\/p>\n
python cosole\u304b\u3089\u51fa\u3066\u3001<\/p>\n
$ pip install environment_kernels\r\n<\/code><\/pre>\n
\u3068\u5165\u529b\u3057\u3001Jupyter\u4e0a\u3067\u30ab\u30fc\u30cd\u30eb\u3092\u5207\u308a\u66ff\u3048\u308b\u30d1\u30c3\u30b1\u30fc\u30b8\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002\u6b21\u306b\u3001<\/p>\n
jupyter notebook --generate-config\r\n<\/code><\/pre>\n
\u3067jupyter\u306e\u8a2d\u5b9a\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210\u3002<\/p>\n
~\/.jupyter\/jupyter_notebook_config.py\u306e\u6700\u7d42\u884c\u306b\u4ee5\u4e0b\u306ecode\u3092\u8ffd\u8a18\u3002<\/p>\n
c.NotebookApp.kernel_spec_manager_class = 'environment_kernels.EnvironmentKernelSpecManager'\r\nc.EnvironmentKernelSpecManager.env_dirs=['C:\/Program Files\/Anaconda3\/envs\/']\r\n<\/code><\/pre>\n
pip install jupyter\r\n<\/code><\/pre>\n
\u3067jupyter\u3092install\u3057\u3066\u3001<\/p>\n
jupyter notebook\r\n<\/code><\/pre>\n
\u3067jupyter-notebook\u3092\u8d77\u52d5\u3055\u305b\u308b\u3002
\n\u3059\u308b\u3068my-rdkit-env\u3092\u9078\u3079\u308b\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u307e\u3059\u3002<\/p>\n
\"\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8<\/div>\n
\u30d9\u30f3\u30bc\u30f3\u3092\u63cf\u304f<\/h1>\n
\u3055\u3042\u3001\u3064\u3044\u306bjupyter-notebook\u3067\u30d9\u30f3\u30bc\u30f3\u3092\u63cf\u304f\u3068\u3053\u308d\u307e\u3067\u304d\u307e\u3057\u305f\uff01
\n\u4ee5\u4e0b\u306e\u30b3\u30fc\u30c9\u3067benzene\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n
from rdkit import Chem\r\nfrom rdkit.Chem import Draw\r\nbenzene = Chem.MolFromSmiles('C1=CC=CC=C1')\r\nDraw.MolToImage(benzene)\r\n<\/code><\/pre>\n
\"benzene.png\"<\/div>\n
\u305f\u3060\u3001\u5c11\u3057\u8868\u793a\u304c\u6c5a\u3044\u3067\u3059\u306d…
\n\u672c\u6765\u306f\u8907\u6570\u5206\u5b50\u3092\u8868\u793a\u3059\u308bmethod\u3067\u3059\u304c\u3001MolsToGridImage\u3092\u4f7f\u3048\u3070\u7dba\u9e97\u306b\u8868\u793a\u3067\u304d\u307e\u3059\u3002<\/p>\n
Draw.MolsToGridImage([benzene])\r\n<\/code><\/pre>\n
\"benzene2.png\"<\/div>\n
pubchempy\u304b\u3089\u53d6\u5f97\u3057\u305f\u60c5\u5831\u3067\u3082\u69cb\u9020\u5f0f\u3092\u63cf\u304f\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002
\n\u305f\u3060\u3057\u3001pcp.get_compounds\u3067\u53d6\u5f97\u3057\u305f\u3082\u306e\u306fpubchempy.Compound\u578b\u306elist\u3067\u3042\u308ardkit.Chem.rdchem.Mol\u3068\u306f\u7570\u306a\u308a\u307e\u3059\u3002\u305d\u306e\u305f\u3081\u8981\u7d20\u3092\u53d6\u308a\u51fa\u3057\u3001smiles\u8a18\u6cd5\u3092\u4ecb\u3057\u3066rdkit.Chem.rdchem.Mol\u306b\u5909\u63db\u3057\u307e\u3059\u3002<\/p>\n
import pubchempy as pcp\r\ntmp = pcp.get_compounds('benzene', 'name')[0]\r\nbenzene = Chem.MolFromSmiles(tmp.isomeric_smiles)\r\nDraw.MolsToGridImage([benzene])\r\n<\/code><\/pre>\n
\"benzene2.png\"<\/div>\n
\u3053\u306e\u65b9\u6cd5\u3092\u7528\u3044\u308c\u3070\u3001\u5316\u5408\u7269\u540d\u304c\u3042\u308c\u3070\u3001smiles\u8a18\u6cd5\u3067\u6307\u5b9a\u3057\u306a\u304f\u3068\u3082\u69d8\u3005\u306a\u5206\u5b50\u3092\u8868\u793a\u3067\u304d\u307e\u3059\u3002<\/p>\n
tmp = pcp.get_compounds('anthracene', 'name')[0]\r\nanthracene = Chem.MolFromSmiles(tmp.isomeric_smiles)\r\nDraw.MolsToGridImage([anthracene])\r\n<\/code><\/pre>\n
\"anthracene.png\"<\/div>\n
\u3055\u3089\u306b\u3001png\u30d5\u30a1\u30a4\u30eb\u4fdd\u5b58\u3082\u3067\u304d\u307e\u3059\u3002
\n\u305f\u3060\u3001\u5c11\u3057\u30c0\u30b5\u3044\u8868\u793a\u306e\u65b9(Chem.Draw.NolTOImage)\u3067\u3059\u306d…
\njupiter-notebook\u4e0a\u306e\u753b\u50cf\u3092\u4fdd\u5b58\u3057\u305f\u65b9\u304c\u826f\u3044\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u3002<\/p>\n
Draw.MolToFile(benzene, 'benzene.png')\r\n<\/code><\/pre>\n
\"benzene.png\"<\/div>\n
\u53c2\u8003<\/h1>\n
RDKit\u516c\u5f0f\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8
\nPubChemPy\u516c\u5f0f\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8
\nAnaconda\u3067\u4f5c\u3063\u305f\u4eee\u60f3\u74b0\u5883\u3092jupiter notebook\u3067\u4f7f\u3046\u65b9\u6cd5<\/p>\n","protected":false},"excerpt":{"rendered":"
\u6982\u8981 chemoinfomatics\u3067\u4f7f\u308f\u308c\u308bpython\u306emodule\u306eRDKit\u3092jupyter-note […]<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-46413","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"yoast_head":"\n- Blog - Silicon Cloud<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/\" \/>\n<meta property=\"og:locale\" content=\"zh_CN\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:description\" content=\"\u6982\u8981 chemoinfomatics\u3067\u4f7f\u308f\u308c\u308bpython\u306emodule\u306eRDKit\u3092jupyter-note […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/\" \/>\n<meta property=\"og:site_name\" content=\"Blog - Silicon Cloud\" \/>\n<meta property=\"article:published_time\" content=\"2023-02-05T18:14:41+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-05-04T07:56:07+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/cdn.silicloud.com\/blog-img\/blog\/img\/657d647137434c4406d04664\/30-0.png\" \/>\n<meta name=\"author\" content=\"\u97f5, \u79d1\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"\u4f5c\u8005\" \/>\n\t<meta name=\"twitter:data1\" content=\"\u97f5, \u79d1\" \/>\n\t<meta name=\"twitter:label2\" content=\"\u9884\u8ba1\u9605\u8bfb\u65f6\u95f4\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 \u5206\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/\",\"url\":\"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/\",\"name\":\"- Blog - Silicon Cloud\",\"isPartOf\":{\"@id\":\"https:\/\/www.silicloud.com\/zh\/blog\/#website\"},\"datePublished\":\"2023-02-05T18:14:41+00:00\",\"dateModified\":\"2024-05-04T07:56:07+00:00\",\"author\":{\"@id\":\"https:\/\/www.silicloud.com\/zh\/blog\/#\/schema\/person\/6530331a63adef3b3443a1fab53a0e6e\"},\"inLanguage\":\"zh-Hans\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.silicloud.com\/zh\/blog\/46413-2\/\"]}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.silicloud.com\/zh\/blog\/#website\",\"url\":\"https:\/\/www.silicloud.com\/zh\/blog\/\",\"name\":\"Blog - 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