{"id":2705,"date":"2025-06-19T10:36:44","date_gmt":"2025-06-19T01:36:44","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=2705"},"modified":"2025-07-10T13:29:54","modified_gmt":"2025-07-10T04:29:54","slug":"gesim_similarity","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2025\/06\/19\/gesim_similarity\/","title":{"rendered":"GESim\u306b\u3088\u308b\u5206\u5b50\u985e\u4f3c\u6027\u8a55\u4fa1"},"content":{"rendered":"\n<p>\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u91d1\u5b50\u4fe1\u4eba\u3067\u3059\u3002<br>\u4eca\u56de\u306f\u5206\u5b50\u985e\u4f3c\u6027\u8a55\u4fa1\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306eGESim\u306e\u7d39\u4ecb\u3092\u3057\u3066\u3044\u304d\u307e\u3059\u3002<\/p>\n\n\n\n<p>\u53c2\u8003\u6587\u732e<br>GESim: ultrafast graph-based molecular similarity calculation via von Neumann graph entropy<br>(Hiroaki Shiokawa, Shoichi Ishida, Kei Terayama, <em>Journal of Cheminformatics<\/em>, <strong>2025<\/strong>, <em>17<\/em>, 57)<br><a href=\"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-025-01003-6\">https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-025-01003-6<\/a><\/p>\n\n\n\n<p>\u52d5\u4f5c\u74b0\u5883<br>Intel Core i7-1265U<br>Windows 11 Pro<br>conda 25.3.1<\/p>\n\n\n\n<p>\u5206\u5b50\u985e\u4f3c\u6027\u3068\u306f\u5bfe\u8c61\u3068\u306a\u308b\u5206\u5b50\u540c\u58eb\u304c\u3001\u69cb\u9020\u7684\u30fb\u6a5f\u80fd\u7684\u306b\u3069\u306e\u7a0b\u5ea6\u4f3c\u901a\u3063\u3066\u3044\u308b\u304b\u3068\u3044\u3046\u6307\u6a19\u306b\u306a\u308a\u307e\u3059\u3002\u3053\u308c\u306f\u300c\u985e\u4f3c\u3057\u305f\u5316\u5408\u7269\u306f\u985e\u4f3c\u3057\u305f\u6027\u8cea\u3092\u6301\u3064 (similar property principle)\u300d<sup>\u203b1<\/sup>\u3068\u3044\u3046\u6982\u5ff5\u306b\u57fa\u3065\u3044\u3066\u304a\u308a\u3001\u5275\u85ac\u7814\u7a76\u306b\u304a\u3044\u3066\u306f\u65e2\u5b58\u85ac\u3068\u306e\u985e\u4f3c\u6027\u3092\u8a55\u4fa1\u3059\u308b\u3053\u3068\u3067\u540c\u7b49\u306e\u85ac\u52b9\u3092\u793a\u3059\u5316\u5408\u7269\u306e\u63a2\u7d22\u306a\u3069\u306b\u7528\u3044\u3089\u308c\u3066\u3044\u307e\u3059\u3002\u3053\u306e\u985e\u4f3c\u6027\u306e\u8a55\u4fa1\u306b\u306f\u69d8\u3005\u306a\u6307\u6a19\u304c\u7528\u3044\u3089\u308c\u3066\u304a\u308a\u3001\u3082\u3063\u3068\u3082\u4ee3\u8868\u7684\u306aTanimoto\u4fc2\u6570\u3067\u306f\u5206\u5b50\u69cb\u9020\u3092\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306b\u3057\u3001\u305d\u306e\u4e00\u81f4\u5ea6\u5408\u3044\u3092\u8a55\u4fa1\u3059\u308b\u3082\u306e\u306b\u306a\u308a\u307e\u3059\u3002\u4eca\u56de\u7d39\u4ecb\u3059\u308bGESim\u3067\u306fvon Neumann graph entropy\u3092\u7528\u3044\u3066\u5206\u5b50\u306e\u985e\u4f3c\u6027\u3092\u8a55\u4fa1\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">GESim\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n\n\n\n<p>Python\u306e\u4eee\u60f3\u74b0\u5883\u3092\u4f5c\u6210\u3057\u3001GESim\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ conda create -n GESim python=3.11 -y\n$ conda activate GESim\n$ pip install --upgrade git+https:\/\/github.com\/LazyShion\/GESim.git<\/code><\/pre>\n\n\n\n<p>\u5fc5\u8981\u306a\u30d1\u30c3\u30b1\u30fc\u30b8\u304c\u81ea\u52d5\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u3001\u672c\u74b0\u5883\u3067\u306fPillow-11.2.1 gesim-0.0.1 numpy-1.26.4 pybind11-2.11.2 rdkit-2023.9.6\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">GESim\u306e\u5b9f\u884c<\/h2>\n\n\n\n<p>\u30c1\u30e5\u30fc\u30c8\u30ea\u30a2\u30eb\u306b\u3057\u305f\u304c\u3063\u3066\u4f7f\u3063\u3066\u307f\u307e\u3057\u3087\u3046\u3002<br>Python\u306e\u5bfe\u8a71\u30e2\u30fc\u30c9\u3067GESim\u3092\u30a4\u30f3\u30dd\u30fc\u30c8\u3057\u3001\u5316\u5408\u7269\u60c5\u5831\u3092SMILES\u8868\u8a18\u3067\u5165\u529b\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ Python\n&gt;&gt;&gt; from rdkit import Chem\n&gt;&gt;&gt; from gesim import gesim\n&gt;&gt;&gt; mol1 = Chem.MolFromSmiles('Cc1nn(C2CCN(Cc3cccc(C#N)c3)CC2)cc1-c1ccccc1')\n&gt;&gt;&gt; mol2 = Chem.MolFromSmiles('Cc1nn(C2CCN(Cc3cccc(Cl)c3)CC2)cc1-c1ccccc1')\n&gt;&gt;&gt; print(gesim.graph_entropy_similarity(mol1, mol2))\n0.9580227325517037<\/code><\/pre>\n\n\n\n<p>mol1\u306b\u5bfe\u3057\u3001mol2\u306f0.958\u306e\u985e\u4f3c\u5ea6\u3092\u6709\u3057\u3066\u3044\u308b\u3068\u8a55\u4fa1\u3055\u308c\u307e\u3057\u305f\u3002\u30b9\u30b3\u30a2\u306f0-1\u306b\u6b63\u898f\u5316\u3055\u308c\u3001\u5b8c\u5168\u306b\u4e00\u81f4\u3057\u3066\u3044\u308b\u5834\u5408\u306f1\u306b\u306a\u308a\u307e\u3059\u3002<br>\u8907\u6570\u5206\u5b50\u3092\u4e00\u5ea6\u306b\u8a55\u4fa1\u3057\u305f\u3044\u5834\u5408\u306fbatch\u3092\u7528\u3044\u3066\u3001<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>&gt;&gt;&gt; mols = &#091;mol1, mol2, Chem.MolFromSmiles('c1ccc(CN2CCC(n3nccc3-c3ccccc3)CC2)cc1')]\n&gt;&gt;&gt; print(gesim.graph_entropy_similarity_batch(mol1, mols))\n&#091;1.0, 0.9580227325517037, 0.7766178810633495]<\/code><\/pre>\n\n\n\n<p>\u3068\u3059\u308b\u3068mols\u306b\u542b\u307e\u308c\u308b\u3059\u3079\u3066\u306e\u5206\u5b50\u306b\u5bfe\u3057\u3066\u3001mol1\u3068\u306e\u985e\u4f3c\u6027\u304c\u8a55\u4fa1\u3055\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n<p>\u4e00\u81f4\u3057\u3066\u3044\u308b\u90e8\u5206\u69cb\u9020\u3092\u63cf\u753b\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<br>Jupyter Notebook\u3067\u5b9f\u884c\u3057\u3066\u3044\u308b\u5834\u5408\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u3001<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>&gt;&gt;&gt; from rdkit.Chem import Draw\n&gt;&gt;&gt; mol1_matched, mol2_matched = gesim.get_matched_mapping_numbers(mol1, mol2)\n&gt;&gt;&gt; mol1_hal = &#091;i for i, mv in enumerate(mol1_matched) if mv == 1]\n&gt;&gt;&gt; mol2_hal = &#091;i for i, mv in enumerate(mol2_matched) if mv == 1]\n&gt;&gt;&gt; Draw.MolsToGridImage(&#091;mol1, mol2], highlightAtomLists=&#091;mol1_hal, mol2_hal], molsPerRow=2, useSVG=True, subImgSize=(250, 200))<\/code><\/pre>\n\n\n\n<p>Windows PowerShell\u7b49\u3067\u5b9f\u884c\u3057\u3066\u3044\u308b\u5834\u5408\u306f\u6700\u7d42\u884c\u3092\u3001<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>&gt;&gt;&gt; img = Draw.MolsToGridImage(&#091;mol1, mol2], highlightAtomLists=&#091;mol1_hal, mol2_hal], molsPerRow=2, useSVG=False, subImgSize=(250, 200))\n&gt;&gt;&gt; img.show()<\/code><\/pre>\n\n\n\n<p>\u3068\u3057\u3066\u5b9f\u884c\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"500\" height=\"200\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image.png\" alt=\"\" class=\"wp-image-2707\" style=\"width:840px;height:auto\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image.png 500w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-300x120.png 300w\" sizes=\"auto, (max-width: 500px) 100vw, 500px\" \/><\/figure>\n\n\n\n<p>\u7d50\u679c\u306f\u3053\u306e\u3088\u3046\u306b\u4e00\u81f4\u3057\u3066\u3044\u308b\u539f\u5b50\u304c\u30cf\u30a4\u30e9\u30a4\u30c8\u3055\u308c\u3066\u8868\u793a\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n<p>GESim\u3067\u306f\u3069\u3046\u3044\u3063\u305f\u30d1\u30e9\u30e1\u30fc\u30bf\u304c\u91cd\u8996\u3055\u308c\u308b\u306e\u304b\u3001\u3044\u304f\u3064\u304b\u306e\u5206\u5b50\u3092\u6bd4\u8f03\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<br>\u307e\u305a\u306f\u30d9\u30f3\u30bc\u30f3\u306e\u7f6e\u63db\u4f53\u3092\u8a55\u4fa1\u3057\u3066\u307f\u307e\u3059\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"333\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-1-1024x333.png\" alt=\"\" class=\"wp-image-2709\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-1-1024x333.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-1-300x98.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-1-768x250.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-1-850x276.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-1.png 1027w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>\u30c8\u30eb\u30a8\u30f3\u306b\u5bfe\u3057\u30a2\u30cb\u30ea\u30f3\u3067\u306f0.752\u3068\u8a55\u4fa1\u3055\u308c\u307e\u3057\u305f\u3002\u30a2\u30cb\u30bd\u30fc\u30eb\u3067\u306f\u91cd\u539f\u5b50\u304c1\u3064\u591a\u3044\u305f\u3081\u304b\u3084\u3084\u4f4e\u304f\u306a\u308a\u307e\u3057\u305f\u3002\u4e00\u65b9\u30cf\u30ed\u30b2\u30f3\u7f6e\u63db\u4f53\u3067\u306f\u3059\u3079\u3066\u540c\u3058\u30b9\u30b3\u30a2\u3067\u8a55\u4fa1\u3055\u308c\u307e\u3057\u305f\u3002\u3053\u306e\u3053\u3068\u304b\u3089\u96fb\u5b50\u5bc6\u5ea6\u3084\u539f\u5b50\u30b5\u30a4\u30ba\u306a\u3069\u306f\u985e\u4f3c\u6027\u306e\u8a55\u4fa1\u306b\u542b\u307e\u308c\u3066\u3044\u306a\u3044\u3053\u3068\u304c\u63a8\u5bdf\u3055\u308c\u307e\u3059\u3002<br>\u6b21\u306bBioisostere\uff08\u751f\u7269\u5b66\u7684\u7b49\u4fa1\u4f53\uff09\u306b\u3064\u3044\u3066\u8a55\u4fa1\u3057\u3066\u307f\u307e\u3059\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"227\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-2-1024x227.png\" alt=\"\" class=\"wp-image-2710\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-2-1024x227.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-2-300x67.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-2-768x170.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-2-850x188.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/06\/image-2.png 1317w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>\u4ee3\u8868\u7684\u306aBioisostere\u3068\u3057\u3066\u30a2\u30df\u30c9\u7d50\u5408\u3092\u30c8\u30ea\u30a2\u30be\u30fc\u30eb\u306b\u3001\u30d9\u30f3\u30bc\u30f3\u3092\u30d3\u30b7\u30af\u30ed\u30da\u30f3\u30bf\u30f3\u306b\u3001\u30ab\u30eb\u30dc\u30f3\u9178\u3092\u30c6\u30c8\u30e9\u30be\u30fc\u30eb\u306b\u5909\u63db\u3057\u305f\u3082\u306e\u3092\u8a55\u4fa1\u3057\u307e\u3057\u305f\u3002\u3044\u305a\u308c\u306e\u5834\u5408\u3082\u7b49\u4fa1\u4f53\u306b\u3088\u308b\u985e\u4f3c\u6027\u8a55\u4fa1\u306e\u52a0\u70b9\u306f\u4f4e\u3044\u3088\u3046\u3067\u3059\u3002\u30b9\u30b3\u30a2\u306e\u9055\u3044\u306f\u524d\u80052\u3064\u304c\u69cb\u9020\u4e2d\u5fc3\u306e\u3042\u308b\u306e\u306b\u5bfe\u3057\u3001\u5f8c\u8005\u306f\u69cb\u9020\u672b\u7aef\u306b\u3042\u308b\u305f\u3081\u3068\u63a8\u5bdf\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u304a\u308f\u308a\u306b<\/h2>\n\n\n\n<p>\u4eca\u56de\u7d39\u4ecb\u3057\u305fGESim\u306f\u975e\u5e38\u306b\u9ad8\u901f\u3067\u3001\u30e9\u30c3\u30d7\u30c8\u30c3\u30d7\u30d1\u30bd\u30b3\u30f3\u3067\u3082\u77ac\u6642\u306b\u7d50\u679c\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u305d\u306e\u305f\u3081\u5927\u898f\u6a21\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304b\u3089\u306e\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u306b\u304a\u3044\u3066\u3082\u6709\u7528\u3060\u3068\u601d\u308f\u308c\u307e\u3059\u3002\u4e00\u65b9\u3067\u5316\u5408\u7269\u306e\u96fb\u5b50\u5bc6\u5ea6\u3084\u5d69\u9ad8\u3055\u306f\u985e\u4f3c\u6027\u306b\u8a55\u4fa1\u3055\u308c\u306a\u3044\u3053\u3068\u304b\u3089\u3001\u305d\u3046\u3044\u3063\u305f\u30d1\u30e9\u30e1\u30fc\u30bf\u3092\u91cd\u8996\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u5834\u5408\u306f\u5225\u306e\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u9078\u629e\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<p>\u203b1 Johnson MA, Maggiora GM, (1990) Concepts and applications of molecular similarity. Wiley, New York.<\/p>\n\n\n\n<p>\u524d\u56de\u8a18\u4e8b<br>AiZynthFinder\u306b\u3088\u308b\u9006\u5408\u6210\u89e3\u6790<br><a href=\"https:\/\/www.insilico.jp\/blog\/2025\/06\/05\/aizynthfinder_retrosynthesis\/\">https:\/\/www.insilico.jp\/blog\/2025\/06\/05\/aizynthfinder_retrosynthesis\/<\/a><br>\u6b21\u56de\u8a18\u4e8b<br>Direct MaxFlux\u6cd5\u306b\u3088\u308b\u9077\u79fb\u72b6\u614b\u4e88\u6e2c<br><a href=\"https:\/\/www.insilico.jp\/blog\/2025\/07\/10\/direct-maxflux\/\">https:\/\/www.insilico.jp\/blog\/2025\/07\/10\/direct-maxflux\/<\/a><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u91d1\u5b50\u4fe1\u4eba\u3067\u3059\u3002\u4eca\u56de\u306f\u5206\u5b50\u985e\u4f3c\u6027\u8a55\u4fa1\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306eGESim\u306e\u7d39\u4ecb\u3092\u3057\u3066\u3044\u304d\u307e\u3059\u3002 \u53c2\u8003\u6587\u732eGESim: ultrafast graph-based molecular similarity calcula&#8230;<\/p>\n","protected":false},"author":7,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[118],"tags":[97],"class_list":["post-2705","post","type-post","status-publish","format-standard","hentry","category-ai-drug-discovery","tag-python"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - 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