{"id":1302,"date":"2021-04-01T11:36:03","date_gmt":"2021-04-01T02:36:03","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1302"},"modified":"2022-02-22T14:39:19","modified_gmt":"2022-02-22T05:39:19","slug":"rdkit_c_programming_similarity_search","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2021\/04\/01\/rdkit_c_programming_similarity_search\/","title":{"rendered":"RDKit\u3067\u3082C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff5e"},"content":{"rendered":"\n<p>\u3000\u4eca\u56de\u306e\u8a71\u984c\u306f<a href=\"https:\/\/www.insilico.jp\/blog\/2021\/03\/18\/openbabel_c_programming_similarity_search_1\/\">\u524d\u56de<\/a>\u304b\u3089\u5f15\u304d\u7d9a\u304d\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff08Similarity Search\uff09\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u30bf\u30a4\u30c8\u30eb\u901a\u308a\u3001RDKit\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3059\u308b\u3068\u3044\u3046\u5185\u5bb9\u3067\u3059\u3002RDKit\u3092\u53d6\u308a\u4e0a\u3052\u308b\u306e\u306f\u521d\u3081\u3066\u3067\u3001\u30d6\u30ed\u30b0\u3063\u3066\u4f55\u3092\u66f8\u304f\u304b\u6bce\u56de\u60a9\u3080\u306e\u3067\u3059\u304c\u3001\u8272\u3005\u3068\u5fd8\u308c\u306a\u3044\u3046\u3061\u306b\u985e\u4f3c\u69cb\u9020\u691c\u7d22\u3059\u308b\u3068\u3044\u3046\u30cd\u30bf\u306b\u3057\u307e\u3057\u305f\u3002<\/p>\n\n\n\n<!--more-->\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u306f\u3058\u3081\u306b\">\u306f\u3058\u3081\u306b<\/h2>\n\n\n\n<p>\u3000\u30b1\u30e2\u30a4\u30f3\u30d5\u30a9\u30de\u30c6\u30a3\u30af\u30b9\u306e\u30c4\u30fc\u30eb\u30ad\u30c3\u30c8\u3068\u3057\u3066\u826f\u304f\u5229\u7528\u3055\u308c\u308b\u306e\u306fRDKit\u3067\u3042\u308a\u3001OpenBabel\u306f\u5c11\u6570\u6d3e\u306a\u6c17\u304c\u3057\u307e\u3059\u3002RDKit\u306fPython\u3068\u975e\u5e38\u306b\u76f8\u6027\u304c\u826f\u3044\u306e\u3067\u3001\u4f7f\u3044\u3084\u3059\u3044\u306e\u3053\u3068\u304c\u7406\u7531\u306e\u4e00\u3064\u306b\u6319\u3052\u3089\u308c\u308b\u3067\u3057\u3087\u3046\u3002\u305d\u308c\u306f\u6050\u3089\u304f\u3001RDKit\u306fPython\u3092\u901a\u3057\u3066\u5229\u7528\u3059\u308b\u3053\u3068\u3092\u524d\u63d0\u3068\u3057\u305f\u8a2d\u8a08\u306b\u306a\u3063\u3066\u304a\u308a\u3001Python\u304c\u6628\u4eca\u306eAI\u30d6\u30fc\u30e0\u3067\u4eba\u6c17\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u8a00\u8a9e\u306b\u306a\u3063\u305f\u3053\u3068\u3068\u3082\u7121\u95a2\u4fc2\u3067\u306f\u7121\u3044\u3067\u3057\u3087\u3046\u3002\u3067\u306f\u306a\u305cOpenBabel\u3070\u304b\u308a\u53d6\u308a\u4e0a\u3052\u3066\u304d\u305f\u304b\u3068\u3044\u3046\u3068\u3001C++\u3067RDKit\u3092\u53d6\u308a\u6271\u3046\u306e\u306f\u5c11\u3005\u9762\u5012\u3060\u304b\u3089\u3067\u3059\u3002\u5148\u305a\u3001C++\u306b\u95a2\u3059\u308b\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8\u304c\u5c11\u306a\u3044\u3067\u3059\u3002\u4ed5\u65b9\u306a\u3044\u304b\u3089\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u3092\u8aad\u3080\u306e\u3067\u3059\u304c\u3001RDKit\u306e\u5834\u5408\u306f\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u304c\u8272\u3005\u306a\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u6563\u3089\u3070\u3063\u3066\u3044\u3066\u3001OpenBabel\u3088\u308a\u3082\u30af\u30e9\u30b9\u306e\u4f7f\u3044\u65b9\u3092\u8abf\u3079\u308b\u306e\u306b\u82e6\u52b4\u3057\u307e\u3059\u3002\u305d\u3082\u305d\u3082\u3069\u306e\u3088\u3046\u306a\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3092\u30a4\u30f3\u30af\u30eb\u30fc\u30c9\u3059\u308c\u3070\u826f\u3044\u304b\uff1f\u305d\u3057\u3066\u30d3\u30eb\u30c9\u3059\u308b\u3068\u304d\u306b\u30ea\u30f3\u30af\u3059\u3079\u304d\u30e9\u30a4\u30d6\u30e9\u30ea\u306f\u4f55\u306a\u306e\u304b\uff1f\u304c\u5206\u304b\u308a\u305a\u3089\u3044\u306e\u3067\u3059\u3002Python\u306e\u5834\u5408\u306f\u3053\u306e\u3088\u3046\u306a\u82e6\u52b4\u306f\u4e00\u5207\u306a\u304f\u3001\u3057\u304b\u3082\u65e5\u672c\u8a9e\u306e\u60c5\u5831\u3082\u7d50\u69cb\u30cd\u30c3\u30c8\u4e0a\u306b\u3042\u308a\u3001C++\u3068\u306e\u5dee\u306f\u6b74\u7136\u3067\u3059\u3002\u3057\u304b\u3057\u306a\u304c\u3089\u3001\u6562\u3048\u3066C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u306b\u6311\u6226\u3059\u308b\u306e\u304c\u3053\u306e\u30d6\u30ed\u30b0\u306a\u306e\u3067\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\">\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n\n\n\n<p>\u3000OpenBabel 3.1\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u306bAnaconda\u3092\u5229\u7528\u3057\u307e\u3057\u305f\u304c\u3001RDKit\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3082Anaconda\u3067\u7c21\u5358\u306b\u3067\u304d\u307e\u3059\u3002\u30b3\u30de\u30f3\u30c9\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ conda install rdkit -c rdkit<\/code><\/pre>\n\n\n\n<p>\u901a\u5e38\u306f\u4eee\u60f3\u74b0\u5883\u3092\u4f5c\u6210\u3057\u3066\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3059\u3002\u4f8b\u3048\u3070OpenBabel 3.1\u306e\u3068\u304d\u4f5c\u6210\u3057\u305f&#8221;ob3&#8243;\u3068\u3044\u3046\u4eee\u60f3\u74b0\u5883\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u5834\u5408\u306f\u3001\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u4e00\u65e6\u4eee\u60f3\u74b0\u5883\u3092\u6709\u52b9\u5316\u3057\u3066\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ conda activate ob3\n$ conda install rdkit -c rdkit<\/code><\/pre>\n\n\n\n<p>\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3068\u30e9\u30a4\u30d6\u30e9\u30ea\u306f\u305d\u308c\u305e\u308c<code>$HOME\/anaconda3\/envs\/ob3\/include<\/code>\u306e\u4e0b\u3068<code>$HOME\/anaconda3\/envs\/ob3\/lib<\/code>\u306e\u4e0b\u306b\u683c\u7d0d\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u4eca\u56de\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\">\u4eca\u56de\u306e\u30d7\u30ed\u30b0\u30e9\u30e0<\/h2>\n\n\n\n<p>\u3000\u4eca\u56de\u306eC++\u30d7\u30ed\u30b0\u30e9\u30e0\u306f<a href=\"https:\/\/www.insilico.jp\/blog\/2021\/03\/18\/openbabel_c_programming_similarity_search_1\/\">\u524d\u56de<\/a>\u3068\u540c\u3058\u985e\u4f3c\u69cb\u9020\u691c\u7d22\u8a08\u7b97\u3092RDKit\u3092\u5229\u7528\u3057\u3066\u4f5c\u6210\u3057\u305f\u3082\u306e\u3067\u3059\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u540d\u306f&#8221;<a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/04\/SimSearch_RD.cpp\">SimSearch_RD.cpp<\/a>&#8220;\u3068\u3057\u3066\u3044\u307e\u3059\u3002\u5165\u529b\u30c7\u30fc\u30bf\u306f&#8221;<a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/Fexofenadine.smi\">Fexofenadine.smi<\/a>&#8220;\u3068&#8221;<a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2021\/03\/test19.smi\">test19.smi<\/a>&#8220;\u3067\u3059\u3002\u305d\u308c\u305e\u308c\u306e\u30ea\u30f3\u30af\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u4e0b\u3055\u3044\u3002<\/p>\n\n\n\n<p>C++\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u5185\u5bb9\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>  1 \/\/ C++\n  2 #include &lt;iostream&gt;\n  3 #include &lt;fstream&gt;\n  4 #include &lt;sstream&gt;\n  5 #include &lt;string&gt;\n  6 #include &lt;vector&gt;\n  7 #include &lt;algorithm&gt;\n  8\n  9 \/\/ C\n 10 #include &lt;cstdio&gt;\n 11 #include &lt;cstdlib&gt;\n 12 #include &lt;ctime&gt;\n 13 #include &lt;cstring&gt;\n 14 #include &lt;cmath&gt;\n 15 #include &lt;unistd.h&gt;\n 16\n 17 \/\/ RDKit\n 18 #include &lt;GraphMol\/RDKitBase.h&gt;\n 19 #include &lt;GraphMol\/FileParsers\/MolSupplier.h&gt;\n 20 \/\/ RDKit FingerPrint\n 21 #include &lt;GraphMol\/Fingerprints\/MorganFingerprints.h&gt;\n 22\n 23 using namespace std;\n 24 using namespace RDKit;\n 25\n 26 int main(int argc, char* argv&#91;]) {\n 27   ifstream isd1(\"Fexofenadine.smi\");\n 28   MolSupplier* ms1 = new SmilesMolSupplier(&amp;isd1, true, \"\\t\", 0, 1, false, true);\n 29   ROMOL_SPTR ref = ROMOL_SPTR(ms1-&gt;next());\n 30\n 31   \/\/ calculate fingerprint\n 32   SparseIntVect&lt;boost::uint32_t&gt;* fp_ref = MorganFingerprints::getFingerprint(*ref, 2);\n 33\n 34   ifstream isd2(\"test19.smi\");\n 35   MolSupplier* ms2 = new SmilesMolSupplier(&amp;isd2, true, \"\\t\", 0, 1, false, true);\n 36\n 37   while (true) {\n 38     if (ms2-&gt;atEnd()) break;\n 39     ROMOL_SPTR mol = ROMOL_SPTR(ms2-&gt;next());\n 40     if (!mol) continue;\n 41\n 42     SparseIntVect&lt;boost::uint32_t&gt;* fp_mol = MorganFingerprints::getFingerprint(*mol, 2);\n 43     double Tc = TanimotoSimilarity(*fp_ref, *fp_mol);\n 44     cout &lt;&lt; mol-&gt;getProp&lt;string&gt;(\"_Name\") &lt;&lt; \"\\t\" &lt;&lt; Tc &lt;&lt; endl;\n 45   }\n 46\n 47   return 1;\n 48 } <\/code><\/pre>\n\n\n\n<p>\u3000\u3044\u3064\u3082\u306e\u3088\u3046\u306b\u7c21\u5358\u306b\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u89e3\u8aac\u3092\u3057\u307e\u3059\u3002\u5148\u305a\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u306f17&#8211;21\u884c\u76ee\u3067\u30a4\u30f3\u30af\u30eb\u30fc\u30c9\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u306f\u6700\u4f4e\u9650\u306e\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3057\u304b\u3042\u308a\u307e\u305b\u3093\u304c\u3001RDKit\u306e\u5229\u7528\u3057\u305f\u3044\u6a5f\u80fd\u306e\u3088\u3063\u3066\u9069\u5207\u306a\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3092\u8ffd\u52a0\u3057\u306a\u3044\u3068\u3044\u3051\u307e\u305b\u3093\u3002\u3057\u304b\u3057\u306a\u304c\u3089\u3001\u3069\u3053\u304b\u306e\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8\u306b\u5206\u304b\u308a\u3084\u3059\u304f\u307e\u3068\u307e\u3063\u3066\u3044\u306a\u3044\u306e\u3067\u3001RDKit\u306e\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u3092\u8aad\u307f\u306a\u304c\u3089\u63a2\u3059\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<p>SMILES\u30d5\u30a1\u30a4\u30eb\u306e\u8aad\u307f\u8fbc\u307f\u306b\u3064\u3044\u3066\u306f27&#8211;29\u884c\u76ee\u306b\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002\u5148\u305a27\u884c\u76ee\u306e\u3088\u3046\u306b\u3001\u666e\u901a\u306b\u30d5\u30a1\u30a4\u30eb\u3092\u30aa\u30fc\u30d7\u30f3\u3057\u307e\u3059\u3002\u6b21\u306e28\u884c\u76ee\u3067\u306f\u3001\u5206\u5b50\u3092\u8aad\u307f\u8fbc\u3080\u305f\u3081\u306e\u30af\u30e9\u30b9\u3067\u3042\u308b&#8221;MolSupplier&#8221;\u306e\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9\u3092\u4f5c\u6210\u3057\u307e\u3059\u3002MolSupplier\u30af\u30e9\u30b9\u3092\u7d99\u627f\u3059\u308b\u5f62\u3067SMILES\u3092\u8aad\u307f\u8fbc\u3080\u30af\u30e9\u30b9\u3067\u3042\u308bSmilesMolSupplier\u304c\u7528\u610f\u3055\u308c\u3066\u3044\u307e\u3059\u3002SD\u30d5\u30a1\u30a4\u30eb\u306e\u5834\u5408\u306fSDMolSupplier\u30af\u30e9\u30b9\u3092\u5229\u7528\u3057\u3066\u3001PDB\u306e\u5834\u5408\u306fPDBMolSupplier\u30af\u30e9\u30b9\u3092\u5229\u7528\u3057\u307e\u3059\u3002\u6700\u5f8c\u306b29\u884c\u76ee\u3067ref\u3068\u3044\u3046\u5909\u6570\u306b\u5206\u5b50\uff08Fexofenadine\uff09\u60c5\u5831\u3092\u683c\u7d0d\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u3053\u3067ROMOL_SPTR\u3068\u3044\u3046\u578b\u304c\u51fa\u3066\u304d\u3066\u3044\u307e\u3059\u3002RDKit\u306b\u306fROMol\u3068\u3044\u3046\u5206\u5b50\u7528\u306e\u30af\u30e9\u30b9\uff08OpenBabel\u3067\u3044\u3046\u3068\u3053\u308d\u306eOBMol\u306e\u3053\u3068\u3067\u3059\uff09\u304c\u3042\u308a\u3001\u3053\u306e\u30af\u30e9\u30b9\u306e\u30b9\u30de\u30fc\u30c8\u30dd\u30a4\u30f3\u30bf\u3092\u793a\u3059\u578b\u3068\u3057\u3066ROMOL_SPTR\u304c\u5b9a\u7fa9\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u81ea\u5206\u3067\u30e1\u30e2\u30ea\u7ba1\u7406\u3059\u308b\u81ea\u4fe1\u304c\u3042\u308b\u306a\u3089<code>ROMol* ref=ms1-&gt;next()<\/code>\u3068\u3057\u3066\u3082\u826f\u3044\u304b\u3068\u601d\u3044\u307e\u3059\u304c\u3001\u306a\u308b\u3079\u304f\u30b9\u30de\u30fc\u30c8\u30dd\u30a4\u30f3\u30bf\u3092\u5229\u7528\u3057\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n<p>\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306e\u8a08\u7b97\u306f32\u884c\u76ee\u3067\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u683c\u7d0d\u3059\u308b\u5909\u6570\u578b\u306f&#8221;SparseIntVect&#8221;\u3067\u3059\u3002&#8221;MorganFingerprints::getFingerprint&#8221;\u3068\u3044\u3046\u95a2\u6570\u3067\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u8a08\u7b97\u3057\u3066\u3001\u7d50\u679c\u3092\u30dd\u30a4\u30f3\u30bf\u3068\u3057\u3066\u8fd4\u3057\u3066\u3044\u307e\u3059\u3002\u305d\u3057\u306643\u884c\u76ee\u3067\u3001\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u304b\u3089\u8c37\u672c\u4fc2\u6570\u3092\u8a08\u7b97\u3057\u3066\u3044\u307e\u3059\u3002Similarity metric\u306b\u3064\u3044\u3066\u306f\u3001\u4ed6\u306b\u3082DiceSimilarity\u3068TverskySimilarity\u304c\u5229\u7528\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u30b3\u30f3\u30d1\u30a4\u30eb\u3068\u5b9f\u884c\">\u30b3\u30f3\u30d1\u30a4\u30eb\u3068\u5b9f\u884c<\/h2>\n\n\n\n<p>\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u30b3\u30f3\u30d1\u30a4\u30eb\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u30b3\u30de\u30f3\u30c9\u3067\u5b9f\u884c\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>g++ -std=c++11 -w SimSearch_RD.cpp -I ${HOME}\/anaconda3\/envs\/ob3\/include\/rdkit \\\n    -L ${HOME}\/anaconda3\/envs\/ob3\/lib \\\n    -Wl,-rpath=${HOME}\/anaconda3\/envs\/ob3\/lib \\\n    -lRDKitFileParsers -lRDKitRDGeneral -lRDKitFingerprints<\/code><\/pre>\n\n\n\n<p>\u6ce8\u610f\u3057\u3066\u307b\u3057\u3044\u306e\u306fg++(gcc)\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u3067\u3059\u3002CentOS7\u3067\u6a19\u6e96\u7684\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u308bgcc\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u3067\u306f\u30b3\u30f3\u30d1\u30a4\u30eb\uff08\u30ea\u30f3\u30af\uff09\u3067\u304d\u307e\u305b\u3093\u3002\u3082\u3063\u3068\u65b0\u3057\u3044\u30d0\u30fc\u30b8\u30e7\u30f3\u3092\u5229\u7528\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u3061\u306a\u307f\u306b\u79c1\u304c\u4f7f\u7528\u3057\u3066\u3044\u308bgcc\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u306f9.3.0\u3067\u3059\u3002Ubuntu 20.04 LTS\u3067\u666e\u901a\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u308b\u3082\u306e\u3067\u3059\u3002<\/p>\n\n\n\n<p>\u3000\u30b3\u30f3\u30d1\u30a4\u30eb\u3057\u3066\u51fa\u6765\u305f\u30ed\u30fc\u30c9\u30e2\u30b8\u30e5\u30fc\u30eb\u3092\u5b9f\u884c\u3059\u308b\u3068\u6b21\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ .\/a.out\n101845628 0.267974\n123506854 0.735537\n139808122 0.486301\n141260304 0.827586\n14677762  0.562044\n150332786 0.740458\n150598871 0.692857\n150622200 0.773109\n150794865 0.736842\n22667272  0.47619\n3348  1\n57619841  0.177033\n57619845  0.21\n57619846  0.164319\n67722853  0.653543\n67767321  0.620155\n68320883  0.521739\n71141694  0.934579\n9936344 0.884956<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u3061\u306a\u307f\u306b\">\u3061\u306a\u307f\u306b<\/h2>\n\n\n\n<p>\u3000\u4e0a\u8a18\u306eC++\u30d7\u30ed\u30b0\u30e9\u30e0\u3092Python\u3067\u4f5c\u6210\u3057\u305f\u3089\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>  1 from rdkit import Chem\n  2 from rdkit.Chem import AllChem\n  3 from rdkit import DataStructs\n  4\n  5 suppl1 = Chem.SmilesMolSupplier(\"Fexofenadine.smi\", delimiter=\"\\t\", titleLine=False)\n  6 ref = next(suppl1)\n  7 fp_ref = AllChem.GetMorganFingerprint(ref, 2)\n  8\n  9 suppl2 = Chem.SmilesMolSupplier(\"test19.smi\", delimiter=\"\\t\", titleLine=False)\n 10 for mol in suppl2:\n 11     fp_mol = AllChem.GetMorganFingerprint(mol, 2)\n 12     Tc = DataStructs.TanimotoSimilarity(fp_ref, fp_mol)\n 13     print(\"%s\\t%f\" % (mol.GetProp(\"_Name\"), Tc))<\/code><\/pre>\n\n\n\n<p>\u5358\u7d14\u306b\u884c\u6570\u3060\u3051\u3092\u6bd4\u8f03\u3057\u3066\u30823\u500d\u4ee5\u4e0a\u77ed\u3044\u3067\u3059\u3002\u3057\u304b\u3082\u3001\u30b3\u30f3\u30d1\u30a4\u30eb\u306e\u5fc5\u8981\u3082\u3042\u308a\u307e\u305b\u3093\u3002\u9069\u5f53\u306b&#8221;SimSearch.py&#8221;\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u540d\u3067\u4e0a\u8a18\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u4fdd\u5b58\u3057\u305f\u3068\u3057\u3066\u3001\u305d\u308c\u3092\u5b9f\u884c\u3059\u308b\u306b\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3060\u3051\u3067\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ python .\/SimSearch.py<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"\u6700\u5f8c\u306b\">\u6700\u5f8c\u306b<\/h2>\n\n\n\n<p>\u3000\u3084\u3063\u3071\u308aRDKit\u306fPython\u3067\u5229\u7528\u3059\u3079\u304d\u3067\u3059\u3002\u79c1\u3082\u3082\u3063\u3068Python\u3092\u52c9\u5f37\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u3000\u4eca\u56de\u306e\u8a71\u984c\u306f\u524d\u56de\u304b\u3089\u5f15\u304d\u7d9a\u304d\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff08Similarity Search\uff09\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u30bf\u30a4\u30c8\u30eb\u901a\u308a\u3001RDKit\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3059\u308b\u3068\u3044\u3046\u5185\u5bb9\u3067\u3059\u3002RDKit\u3092\u53d6\u308a\u4e0a\u3052\u308b\u306e\u306f\u521d\u3081\u3066\u3067\u3001\u30d6\u30ed\u30b0\u3063\u3066\u4f55\u3092\u66f8\u304f\u304b\u6bce\u56de&#8230;<\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[19,33,15],"tags":[70],"class_list":["post-1302","post","type-post","status-publish","format-standard","hentry","category-linux","category-rdkit","category-15","tag-similarity-search"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.3.1 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>RDKit\u3067\u3082C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff5e - In Silico \u5275\u85ac<\/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.insilico.jp\/blog\/2021\/04\/01\/rdkit_c_programming_similarity_search\/\" \/>\n<meta property=\"og:locale\" content=\"ja_JP\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"RDKit\u3067\u3082C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff5e - In Silico \u5275\u85ac\" \/>\n<meta property=\"og:description\" content=\"\u3000\u4eca\u56de\u306e\u8a71\u984c\u306f\u524d\u56de\u304b\u3089\u5f15\u304d\u7d9a\u304d\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff08Similarity Search\uff09\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u30bf\u30a4\u30c8\u30eb\u901a\u308a\u3001RDKit\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3059\u308b\u3068\u3044\u3046\u5185\u5bb9\u3067\u3059\u3002RDKit\u3092\u53d6\u308a\u4e0a\u3052\u308b\u306e\u306f\u521d\u3081\u3066\u3067\u3001\u30d6\u30ed\u30b0\u3063\u3066\u4f55\u3092\u66f8\u304f\u304b\u6bce\u56de...\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.insilico.jp\/blog\/2021\/04\/01\/rdkit_c_programming_similarity_search\/\" \/>\n<meta property=\"og:site_name\" content=\"In Silico \u5275\u85ac\" \/>\n<meta property=\"article:published_time\" content=\"2021-04-01T02:36:03+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-02-22T05:39:19+00:00\" \/>\n<meta name=\"author\" content=\"\u682a\u5f0f\u4f1a\u793e\u30a4\u30f3\u30c6\u30fc\u30b8\u30d8\u30eb\u30b9\u30b1\u30a2 \u91d1\u4e95 \u5343\u91cc\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" 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