{"id":1292,"date":"2021-03-22T15:29:22","date_gmt":"2021-03-22T06:29:22","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1292"},"modified":"2022-02-22T14:41:20","modified_gmt":"2022-02-22T05:41:20","slug":"openbabel_c_programming_similarity_search_2","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2021\/03\/22\/openbabel_c_programming_similarity_search_2\/","title":{"rendered":"OpenBabel\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff5e\u3000\u5f8c\u7de8"},"content":{"rendered":"\n<p>\u3000\u4eca\u56de\u306f<a href=\"https:\/\/www.insilico.jp\/blog\/2021\/03\/18\/openbabel_c_programming_similarity_search_1\/\">\u524d\u7de8<\/a>\u306b\u5f15\u304d\u7d9a\u304dOpenBabel\u3092\u5229\u7528\u3057\u305f\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff08Similarity Search\uff09\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u5f8c\u7de8\u3067\u306f\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u89e3\u8aac\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<!--more-->\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u30d7\u30ed\u30b0\u30e9\u30e0\u89e3\u8aac\">\u30d7\u30ed\u30b0\u30e9\u30e0\u89e3\u8aac<\/h2>\n\n\n\n<p>\u3000C++\u30d7\u30ed\u30b0\u30e9\u30e0SimSearch.cpp\u306e\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>  1 #include &lt;fstream&gt;\n  2 #include &lt;iostream&gt;\n  3 #include &lt;iomanip&gt;\n  4 #include &lt;string&gt;\n  5\n  6 #include &lt;openbabel\/mol.h&gt;\n  7 #include &lt;openbabel\/obconversion.h&gt;\n  8 #include &lt;openbabel\/fingerprint.h&gt;\n  9\n 10 using namespace std;\n 11 using namespace OpenBabel;\n 12\n 13 int main(int argc, char* argv&#91;]) {\n 14   OBConversion conv;\n 15   conv.SetInFormat(\"SMI\");\n 16\n 17   \/\/ \u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306e\u8a2d\u5b9a(ECFP4)\n 18   OBFingerprint* pFP = OBFingerprint::FindFingerprint(\"ECFP4\");\n 19   \/\/ OBFingerprint* pFP = OBFingerprint::FindFingerprint(\"MACCS\");\n 20\n 21   \/\/ \u53c2\u7167\u5206\u5b50\u306e\u8aad\u307f\u8fbc\u307f\n 22   ifstream ifs1(\"Fexofenadine.smi\");\n 23   OBMol ref; \n 24   conv.Read(&amp;ref, &amp;ifs1);\n 25   ifs1.close();\n 26\n 27   \/\/ \u53c2\u7167\u5206\u5b50\u306e\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u53d6\u5f97\n 28   vector&lt;unsigned int&gt; fp_ref;\n 29   pFP-&gt;GetFingerprint(&amp;ref, fp_ref);\n 30\n 31   \/\/ \u30c6\u30b9\u30c8\u5206\u5b50\u306e\u8aad\u307f\u8fbc\u307f\u958b\u59cb\n 32   ifstream ifs2(\"test19.smi\");\n 33   vector&lt;unsigned int&gt; fp_mol;\n 34   OBMol mol;\n 35   while (conv.Read(&amp;mol, &amp;ifs2)) {\n 36     \/\/ \u30c6\u30b9\u30c8\u5206\u5b50\u306e\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u53d6\u5f97\u3057\u3066\u8c37\u672c\u4fc2\u6570\u3092\u8a08\u7b97\n 37     pFP-&gt;GetFingerprint(&amp;mol, fp_mol);\n 38     double Tc = OBFingerprint::Tanimoto(fp_ref, fp_mol);\n 39     cout &lt;&lt; mol.GetTitle() &lt;&lt; \"\\t\" &lt;&lt; Tc &lt;&lt; endl;\n 40     \/\/ \u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u30af\u30ea\u30a2\n 41     fp_mol.clear();\n 42   }\n 43   ifs2.close();\n 44\n 45   return 0;\n 46 }<\/code><\/pre>\n\n\n\n<p>\u3000\u5148\u305a8\u884c\u76ee\u3067\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u7528\u306e\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3092include\u3057\u3066\u3044\u307e\u3059\u3002\u305d\u3057\u306618\u884c\u76ee\u3067\u4f7f\u7528\u3059\u308b\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u8a2d\u5b9a\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u306f&#8221;ECFP4&#8243;\u3067\u3059\u304c\u3001\u4ed6\u306b\u3082\u8272\u3005\u5229\u7528\u3067\u304d\u308b\u307f\u305f\u3044\u3067\u3059\u3002\u5229\u7528\u53ef\u80fd\u306a\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306e\u4e00\u89a7\u306f&#8221;obabel&#8221;\u30b3\u30de\u30f3\u30c9\u3067\u8868\u793a\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ obabel -L fingerprints\nECFP0    Extended-Connectivity Fingerprints (ECFPs)\nECFP10    Extended-Connectivity Fingerprints (ECFPs)\nECFP2    Extended-Connectivity Fingerprints (ECFPs)\nECFP4    Extended-Connectivity Fingerprints (ECFPs)\nECFP6    Extended-Connectivity Fingerprints (ECFPs)\nECFP8    Extended-Connectivity Fingerprints (ECFPs)\nFP2    Indexes linear fragments up to 7 atoms.\nFP3    SMARTS patterns specified in the file patterns.txt\nFP4    SMARTS patterns specified in the file SMARTS_InteLigand.txt\nMACCS    SMARTS patterns specified in the file MACCS.txt<\/code><\/pre>\n\n\n\n<p>\u3000\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306e\u8a08\u7b97\u306f28\u300129\u884c\u76ee\u306837\u884c\u76ee\u3067\u5b9f\u884c\u3057\u3066\u3044\u307e\u3059\u3002\u305d\u308c\u305e\u308c\u53c2\u7167\u5316\u5408\u7269\u3068\u30e9\u30a4\u30d6\u30e9\u30ea\u5316\u5408\u7269\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u53c2\u7167\u5316\u5408\u7269\u306e\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306f\u6700\u521d\u306b\u4e00\u5ea6\u8a08\u7b97\u3059\u308c\u3070\u826f\u3044\u306e\u3067\u3001\u30eb\u30fc\u30d7\u306e\u5916\u5074\u3067\u884c\u3063\u3066\u3044\u307e\u3059\u3002\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306e\u60c5\u5831\u3092\u5165\u308c\u308b\u5909\u6570\u306e\u578b\u306f&#8221;vector&#8221;\u3067\u3059\u3002unsigned int\u306e\u30b5\u30a4\u30ba\u306f4\u30d0\u30a4\u30c8\u306a\u306e\u3067\u300132\u30d3\u30c3\u30c8\u3068\u3044\u3046\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002\u4e00\u65b9\u3001OpenBabel\u3067\u8a08\u7b97\u3055\u308c\u308bECFP4\u306e\u30c7\u30d5\u30a9\u30eb\u30c8\u306e\u30d3\u30c3\u30c8\u9577\u306f4096\u3067\u3059\u3002\u3057\u305f\u304c\u3063\u3066\u3001\u3053\u306e\u30d9\u30af\u30bf\u30fc\u306e\u30b5\u30a4\u30ba\u306f128(=4096\/32)\u3068\u3044\u3046\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<p>\u3000Similarity\u3092\u8a08\u7b97\u3059\u308b2\u3064\u306e\u69cb\u9020\u306e\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u304c\u8a08\u7b97\u51fa\u6765\u305f\u3089\u300138\u884c\u76ee\u306e&#8221;OBFingerprint::Tanimoto&#8221;\u3068\u3044\u3046\u95a2\u6570\u3067\u8c37\u672c\u4fc2\u6570\u304c\u8a08\u7b97\u3067\u304d\u307e\u3059\u3002\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u306f\u53c2\u7167\u5316\u5408\u7269\u306e\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306f&#8221;fp_ref&#8221;\u3068\u3044\u3046\u5909\u6570\u306b\u5165\u308c\u3066\u3001\u30e9\u30a4\u30d6\u30e9\u30ea\u5316\u5408\u7269\u306e\u65b9\u306f&#8221;fp_mol&#8221;\u3068\u3044\u3046\u5909\u6570\u306b\u5165\u308c\u3066\u3044\u307e\u3059\u3002\u8c37\u672c\u4fc2\u6570\u4ee5\u5916\u306eSimilarity metric\u304c\u3042\u308b\u306e\u304b\u30bd\u30fc\u30b9\u3092\u78ba\u8a8d\u3057\u3066\u307f\u307e\u3057\u305f\u304c\u3001\u3069\u3046\u3084\u3089\u8c37\u672c\u3057\u304b\u7121\u3044\u307f\u305f\u3044\u3067\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"rdkit\u3068\u306e\u6bd4\u8f03\">RDKit\u3068\u306e\u6bd4\u8f03<\/h2>\n\n\n\n<p>\u3000OpenBabel\u3067\u8a08\u7b97\u3055\u308c\u308bSimilarity\u304c\u3001\u4ed6\u306e\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3067\u306e\u8a08\u7b97\u5024\u3068\u3069\u306e\u7a0b\u5ea6\u306e\u5dee\u304c\u3042\u308b\u304b\u78ba\u8a8d\u3057\u3066\u307f\u307e\u3057\u305f\u3002\u6bd4\u8f03\u5bfe\u8c61\u3068\u3057\u3066\u306f\u3084\u306f\u308aRDKit\u304c\u826f\u3044\u3067\u3057\u3087\u3046\u3002\u3069\u3061\u3089\u3082\u30c7\u30d5\u30a9\u30eb\u30c8\u306e\u8a2d\u5b9a\u3067\u524d\u7de8\u306e\u554f\u984c\u8a2d\u5b9a\u306e\u7bc0\u3067\u793a\u3057\u305f\u8a08\u7b97\u3092\u3084\u3063\u3066\u307f\u307e\u3057\u305f\u3002\u7d50\u679c\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u56f3\u306b\u306a\u308a\u307e\u3059\u3002OpenBabel\u3068RDKit\u3067\u8a08\u7b97\u3055\u308c\u308bSimilarity\u306e\u5024\u304c\u4e00\u81f4\u3059\u308b\u5834\u5408\u306f\u8d64\u7dda\u306b\u4e57\u308b\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-1024x1024.png\" alt=\"\" class=\"wp-image-1289\" width=\"307\" height=\"307\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-1024x1024.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-300x300.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-150x150.png 150w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-768x768.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-1536x1536.png 1536w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-2048x2048.png 2048w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-850x850.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/graph_ob_vs_rdkit-45x45.png 45w\" sizes=\"auto, (max-width: 307px) 100vw, 307px\" \/><figcaption>OpenBabel\u3068RDKit\u3067\u8a08\u7b97\u3055\u308c\u308bECFP4\u306eTanimoto Coef. \u306e\u6bd4\u8f03<\/figcaption><\/figure><\/div>\n\n\n\n<p>\u3000\u3053\u306e\u56f3\u3092\u898b\u308b\u3068\u540c\u3058ECFP4\u3092\u5229\u7528\u3057\u305fSimilarity\u3067\u3042\u308b\u306b\u3082\u304b\u304b\u308f\u3089\u305a\u3001\u7d50\u69cb\u30d0\u30e9\u30c4\u30ad\u304c\u3042\u308b\u3088\u3046\u306b\u898b\u3048\u307e\u3059\u3002\u60f3\u50cf\u3055\u308c\u308b\u30d0\u30e9\u30c4\u30ad\u306e\u7406\u7531\u306f\u3001RDKit\u306eECFP4\u306e\u30d3\u30c3\u30c8\u9577\u3068OpenBabel\u306e\u65b9\u306e\u30d3\u30c3\u30c8\u9577\u304c\u7570\u306a\u308b\u3053\u3068\u304c\u8003\u3048\u3089\u308c\u307e\u3059\u3002\u5b9f\u969b\u3001Openbabel\u306f4096\u30d3\u30c3\u30c8\u3067RDKit\u306e\u65b9\u306f2048\u30d3\u30c3\u30c8\u306b\u306a\u3063\u3066\u3044\u307e\u3059\u3002\u3057\u304b\u3057\u306a\u304c\u3089OpenBabel\u306e\u65b9\u30922048\u30d3\u30c3\u30c8\u306b\u5909\u66f4\u3057\u3066\u8a08\u7b97\u3057\u3066\u3082\u3001\u591a\u5c11\u6570\u5024\u304c\u7570\u306a\u308b\u5316\u5408\u7269\u3082\u3042\u308b\u3068\u3044\u3046\u7a0b\u5ea6\u3067\u3001\u5168\u304f\u6539\u5584\u306f\u898b\u3089\u308c\u306a\u304b\u3063\u305f\u3067\u3059\u3002\u3061\u306a\u307f\u306b\u30d3\u30c3\u30c8\u6570\u306e\u5909\u66f4\u306f&#8221;GetFingerprint(&amp;ref, fp_ref, 2048)&#8221;\u306e\u3088\u3046\u306b\u3001\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u8a08\u7b97\u3059\u308b\u30e1\u30bd\u30c3\u30c9\u3092\u547c\u3073\u51fa\u3059\u6642\u306b\u6307\u5b9a\u3059\u308c\u3070\u826f\u3044\u3067\u3059\u3002<\/p>\n\n\n\n<p>\u3000\u3069\u3046\u3084\u3089\u3001OpenBabel\u3068RDKit\u306e\u9593\u306b\u306f\u8a08\u7b97\u65b9\u6cd5\u306b\u6839\u672c\u7684\u306a\u9055\u3044\u304c\u3042\u308b\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u3002\u60f3\u5b9a\u4ee5\u4e0a\u306b\u30d0\u30e9\u30c4\u30ad\u304c\u5927\u304d\u3044\u7d50\u679c\u3068\u306a\u308a\u307e\u3057\u305f\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" 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