{"id":1277,"date":"2021-03-18T14:42:29","date_gmt":"2021-03-18T05:42:29","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1277"},"modified":"2022-02-22T14:42:42","modified_gmt":"2022-02-22T05:42:42","slug":"openbabel_c_programming_similarity_search_1","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2021\/03\/18\/openbabel_c_programming_similarity_search_1\/","title":{"rendered":"OpenBabel\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff5e\u3000\u524d\u7de8"},"content":{"rendered":"\n

\u3000\u4eca\u56de\u306e\u8a71\u984c\u306fOpenBabel\u3092\u5229\u7528\u3057\u305f\u985e\u4f3c\u69cb\u9020\u691c\u7d22\uff08Similarity Search\uff09\u306b\u3064\u3044\u3066\u3067\u3059\u3002\u3044\u307e\u3069\u304dSimilarity Search\u306a\u3069\u3001\u308f\u3056\u308f\u3056\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3057\u306a\u304f\u3066\u3082\u4f7f\u3044\u52dd\u624b\u306e\u826f\u3044\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306f\u6ca2\u5c71\u3042\u308a\u307e\u3059\u3002\u3055\u3089\u306b\u306fOpenBabel\u306e\u6a19\u6e96\u306e\u30b3\u30de\u30f3\u30c9\u3067\u3082\u7c21\u5358\u306b\u5b9f\u884c\u3067\u304d\u307e\u3059\u3002\u3057\u304b\u3057\u6562\u3048\u3066C++\u3092\u4f7f\u3063\u3066\uff08Python\u3058\u3083\u306a\u304f\u3066\uff09\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3057\u3066Similarity Search\u3057\u305f\u3044\uff01\u3068\u3044\u3046\u5909\u306a\u4eba\u3060\u3051\u4ee5\u4e0b\u306e\u8a73\u7d30\u3092\u8aad\u3093\u3067\u307f\u3066\u304f\u3060\u3055\u3044\u3002\u8a18\u4e8b\u304c\u9577\u304f\u306a\u308a\u305d\u3046\u306a\u306e\u3067\u524d\u5f8c\u7de8\u306b\u5206\u3051\u3066\u304a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n\n\n\n\n

\u306f\u3058\u3081\u306b<\/h2>\n\n\n\n

\u3000\u5275\u85ac\u5316\u5b66\u306b\u306f\u300c\u69cb\u9020\u6d3b\u6027\u76f8\u95a2\u300d\u3068\u3044\u3046\u8a00\u8449\u304c\u5fc5\u305a\u51fa\u3066\u304d\u307e\u3059\u3002\u69cb\u9020\u3068\u6d3b\u6027\u306e\u9593\u306b\u76f8\u95a2\u304c\u3042\u308b\u3068\u3044\u3046\u3053\u3068\u306f\u3001\u69cb\u9020\u5f0f\u304c\u4f3c\u3066\u3044\u308b\u6216\u308b2\u3064\u306e\u5316\u5408\u7269\u3092\u6bd4\u8f03\u3059\u308b\u3068\u751f\u7406\u6d3b\u6027\u3082\u4f3c\u3066\u3044\u308b\u3068\u3044\u3046\u3053\u3068\u3067\u3059\u3002\u4e00\u90e8\u306e\u4f8b\u5916\u3068\u3057\u3066”Activity Cliff”\u3068\u3044\u3046\u73fe\u8c61\u3082\u898b\u3089\u308c\u307e\u3059\u304c\u3001\u69cb\u9020\u6d3b\u6027\u76f8\u95a2\u306f\u6982\u306d\u6b63\u3057\u304f\u3001\u5275\u85ac\u5316\u5b66\u306b\u304a\u3051\u308b\u4e00\u3064\u306e\u539f\u7406\u3067\u3042\u308b\u3068\u601d\u3044\u307e\u3059\u3002\u3057\u305f\u304c\u3063\u3066\u3001\u6d3b\u6027\u304c\u6709\u308b\u3053\u3068\u304c\u5206\u304b\u3063\u3066\u3044\u308b\u5316\u5408\u7269\u306b\u985e\u4f3c\u3057\u305f\u69cb\u9020\u306e\u3082\u306e\u3092\u63a2\u3059\u3053\u3068\u306f\u3001\u5275\u85ac\u306e\u57fa\u672c\u4e2d\u306e\u57fa\u672c\u3068\u3044\u3046\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

\u554f\u984c\u8a2d\u5b9a<\/h2>\n\n\n\n

\u3000\u4f55\u304b\u306e\u85ac\u3092\u4e00\u3064\u4f8b\u306b\u3068\u3063\u3066\u3001\u305d\u306e\u53c2\u7167\u5316\u5408\u7269\u3068\u30e9\u30a4\u30d6\u30e9\u30ea\u4e2d\u306e\u5168\u3066\u306e\u5316\u5408\u7269\u3068\u306eSimilarity\u3092\u8a08\u7b97\u3059\u308b\u3053\u3068\u3092\u76ee\u7684\u306b\u3057\u307e\u3059\u3002\u3053\u306e\u30d6\u30ed\u30b0\u306f3\u6708\u306e\u307e\u3055\u306b\u82b1\u7c89\u304c\u98db\u3093\u3067\u3044\u308b\u6642\u671f\u306b\u66f8\u3044\u3066\u3044\u307e\u3059\u306e\u3067\u3001\u53c2\u7167\u5316\u5408\u7269\u3068\u3057\u3066\u6297\u30d2\u30b9\u30bf\u30df\u30f3\u85ac\u306e\u4e00\u3064\u3067\u3042\u308bFexofenadine\uff08\u30a2\u30ec\u30b0\u30e9\u306a\u3069\uff09\u3068\u3057\u307e\u3059\u3002Similarity\u306e\u5024\u306f\u3001\u69cb\u9020\u5f0f\u3092\u4e00\u65e6\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u306b\u5909\u63db\u3057\u305f\u5f8c\u306b\u3001\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u540c\u58eb\u3092\u6bd4\u8f03\u3057\u3066\u8c37\u672c\u4fc2\u6570\u304c\u8a08\u7b97\u3055\u308c\u307e\u3059\u3002\u3053\u3053\u3067\u306f\u4e00\u822c\u7684\u306b\u5e83\u304f\u5229\u7528\u3055\u308c\u3066\u3044\u308bECFP4\u3068\u3044\u3046\u30d5\u30a3\u30f3\u30ac\u30fc\u30d7\u30ea\u30f3\u30c8\u3092\u5229\u7528\u3059\u308b\u3053\u3068\u306b\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"
Fexofenadine<\/figcaption><\/figure><\/div>\n\n\n\n

\u3000\u3053\u3053\u3067\u7d39\u4ecb\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\u306f”SimSearch.cpp<\/a>“\u3067\u3059\u3002\u30ea\u30f3\u30af\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304f\u3060\u3055\u3044\u3002\u305d\u3057\u3066\u5229\u7528\u3059\u308b\u5316\u5408\u7269\u30d5\u30a1\u30a4\u30eb\u306fSMILES\u5f62\u5f0f\u3067\u3001”Fexofenadine.smi<\/a>“\u3068”test19.smi<\/a>“\u3082\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n

\u7d50\u679c\u304c\u304a\u304b\u3057\u3044\uff1f<\/h2>\n\n\n\n

\u30003\u500b\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u51fa\u6765\u305f\u3089\u30b3\u30f3\u30d1\u30a4\u30eb\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\u30b3\u30de\u30f3\u30c9\u306f\u4ee5\u524d\u306eOpenBabel\u95a2\u9023\u306e\u8a18\u4e8b\u3068\u540c\u3058\u304f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

g++ -std=c++11 SimSearch.cpp -I\/usr\/local\/include\/openbabel-2.0 -L\/usr\/local\/lib -lopenbabel<\/code><\/pre>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u5b9f\u884c\u3059\u308b\u3068\u6b21\u306e\u3088\u3046\u306a\u51fa\u529b\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
$ .\/a.out\n101845628       -1\n123506854       0.482589\n139808122       -1\n141260304       -1\n14677762        -1\n150332786       -1\n150598871       -1\n150622200       0.494637\n150794865       -1\n22667272        -1\n3348    0.730604\n57619841        -1\n57619845        -1\n57619846        -1\n67722853        0.560463\n67767321        0.466235\n68320883        -1\n71141694        -1\n9936344 -1<\/code><\/pre>\n\n\n\n
\u3053\u306e\u7d50\u679c\u306e\u7b2c\u4e00\u5217\u306f\u30c6\u30b9\u30c8\u5316\u5408\u7269\u306eID\u3067\u3001\u7b2c\u4e8c\u5217\u304cFexofenadine\u3068\u306eSimilarity\u306e\u5024\u3068\u306a\u308a\u307e\u3059\u3002\u3057\u304b\u3057\u306a\u304c\u3089-1\u3068\u306a\u3063\u3066\u308b\u3082\u306e\u304c\u591a\u304f\u3001\u4f55\u304b\u304c\u304a\u304b\u3057\u3044\u3067\u3059\u3002\u8272\u3005\u3057\u3089\u3079\u305f\u7d50\u679cOpenBabel\u306eversion 2.4\u3067\u306f\u30c0\u30e1\u3067\u3001\u65b0\u3057\u3044version 3.1\u306b\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u3053\u3068\u304c\u5206\u304b\u308a\u307e\u3057\u305f\u3002<\/p>\n\n\n\n
Anaconda\u6700\u9ad8\uff01<\/h2>\n\n\n\n
\u3000OpenBabel\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u306b\u3064\u3044\u3066\u306f\u4ee5\u524d\u306e\u30d6\u30ed\u30b0<\/a>\u3067\u7d39\u4ecb\u3057\u307e\u3057\u305f\u3002\u305d\u306e\u30d6\u30ed\u30b0\u3092\u5c11\u3057\u8aad\u3093\u3067\u3044\u305f\u3060\u3051\u308c\u3070\u5206\u304b\u308a\u307e\u3059\u304c\u3001OpenBabel\u3092\u6700\u521d\u304b\u3089\u30d3\u30eb\u30c9\u3059\u308b\u306e\u306f\u3068\u3066\u3082\u9762\u5012\u3067\u3059\u3002”CMakeLists.txt”\u3092\u8aad\u3080\u3068\u304b\u4e8c\u5ea6\u3068\u3084\u308a\u305f\u304f\u306a\u3044\u306e\u3067\u3001\u4f55\u304b\u5225\u306e\u65b9\u6cd5\u304c\u306a\u3044\u304b\u306a\u3041\u3068\u8003\u3048\u3066\u3044\u305f\u3089Anaconda\u304c\u4f7f\u3048\u308b\u3053\u3068\u304c\u5206\u304b\u308a\u307e\u3057\u305f\u3002Anaconda\u3092\u5229\u7528\u3057\u305fOpenBabel 3.1\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u624b\u9806\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002\uff08Anaconda\u81ea\u4f53\u306e\u89e3\u8aac\u306f\u3053\u3053\u3067\u306f\u7701\u304d\u307e\u3059\u3002\uff09<\/p>\n\n\n\n
  1. \u30c6\u30ad\u30b9\u30c8\u30a8\u30c7\u30a3\u30bf\u306a\u3069\u3092\u5229\u7528\u3057\u3066\u3001\u4ee5\u4e0b\u306e\u5185\u5bb9\u3092”env.yml”\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u540d\u3067\u4f5c\u6210\u3057\u307e\u3059\u3002<\/li><\/ol>\n\n\n\n
    name: ob3\nchannels:\n  - conda-forge\n  - bioconda\n  - defaults\ndependencies:\n  - openbabel=3.1\n  - python=3.8<\/code><\/pre>\n\n\n\n
    2. \u4ee5\u4e0b\u306econda\u30b3\u30de\u30f3\u30c9\u3067\u4eee\u60f3\u74b0\u5883\u3092\u69cb\u7bc9\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
    $ conda env create -f env.yml<\/code><\/pre>\n\n\n\n
    3. \u4f5c\u6210\u3057\u305f\u4eee\u60f3\u74b0\u5883\u3092\u6709\u52b9\u5316\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
    $ conda activate ob3<\/code><\/pre>\n\n\n\n
    \u4ee5\u4e0a\u306e\u624b\u9806\u3067OpenBabel 3.1\u304c\u5229\u7528\u53ef\u80fd\u306b\u306a\u308a\u307e\u3059\u3002OpenBabel\u306e\u30e9\u30a4\u30d6\u30e9\u30ea\u306f$HOME\/anaconda3\/envs\/ob3\/lib<\/code>\u306e\u4e0b\u306b\u914d\u7f6e\u3055\u308c\u307e\u3059\u3002\u305d\u3057\u3066\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u306f$HOME\/anaconda3\/envs\/ob3\/include<\/code>\u306e\u4e0b\u306b\u914d\u7f6e\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n
    \u3000Anaconda\u3092\u901a\u3057\u3066\u306eC++\u7528\u30e9\u30a4\u30d6\u30e9\u30ea\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u306fOpenBabel\u306b\u9650\u308a\u307e\u305b\u3093\u3002Anaconda\u3063\u3066Python\u5c02\u7528\u306e\u30c4\u30fc\u30eb\u3068\u601d\u3063\u3066\u307e\u3057\u305f\u304c\u3001\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3082\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u308b\u3053\u3068\u3092\u77e5\u3063\u3066\u3001\u300cC++\u30d7\u30ed\u30b0\u30e9\u30de\u30fc\u306b\u3082\u4f7f\u3048\u308b\uff01\u300d\u3068\u611f\u52d5\u3057\u307e\u3057\u305f\u3002\u77e5\u3063\u3066\u3044\u305f\u4eba\u304b\u3089\u3059\u308c\u3070\u4f55\u3092\u5f53\u305f\u308a\u524d\u306e\u3053\u3068\u3067\u611f\u52d5\u3057\u3066\u3044\u308b\u306e\uff1f\u3063\u3066\u611f\u3058\u3067\u3057\u3087\u3046\u3051\u3069\u306d\u3002\u3044\u305a\u308c\u306b\u3057\u3066\u3082\u3001\u9762\u5012\u306a\u30d3\u30eb\u30c9\u3092\u3084\u3089\u306a\u304f\u3066\u3082\u826f\u3044\u306e\u306f\u697d\u3067\u3059\u306d\u3002<\/p>\n\n\n\n
    \u518d\u5ea6\u30b3\u30f3\u30d1\u30a4\u30eb<\/h2>\n\n\n\n
    Anaconda\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\u30d8\u30c3\u30c0\u30fc\u30d5\u30a1\u30a4\u30eb\u3068\u30e9\u30a4\u30d6\u30e9\u30ea\u3092\u5229\u7528\u3057\u3066\u3001C++\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u30b3\u30f3\u30d1\u30a4\u30eb\u3057\u307e\u3059\u3002\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u7c21\u5358\u306a\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n
    g++ -std=c++11 SimSearch.cpp -I${HOME}\/anaconda3\/envs\/ob3\/include\/openbabel3 \\\n    -L${HOME}\/anaconda3\/envs\/ob3\/lib \\\n    -Wl,-rpath=${HOME}\/anaconda3\/envs\/ob3\/lib -l openbabel<\/code><\/pre>\n\n\n\n
    \u3053\u3053\u3067”-Wl,-rpath=\u2026”\u3068\u3044\u3046\u30aa\u30d7\u30b7\u30e7\u30f3\u3092\u6307\u5b9a\u3059\u308b\u3053\u3068\u306b\u3088\u308a\u3001\u7279\u5b9a\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306e.so\u30d5\u30a1\u30a4\u30eb\u3092\u30ea\u30f3\u30af\u3059\u308b\u3053\u3068\u3092\u5f37\u5236\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u308c\u3092\u5165\u308c\u306a\u3044\u3068version 2.4\u306e\u65b9\u306e\u30e9\u30a4\u30d6\u30e9\u30ea\u304c\u30ea\u30f3\u30af\u3055\u308c\u3066\u3057\u307e\u3044\u3001\u8a08\u7b97\u7d50\u679c\u304c\u304a\u304b\u3057\u3044\u307e\u307e\u306b\u306a\u308b\u53ef\u80fd\u6027\u304c\u3042\u308a\u307e\u3059\u3002\u30b3\u30f3\u30d1\u30a4\u30eb\u51fa\u6765\u305f\u3089\u5b9f\u884c\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002
    \u4ee5\u4e0b\u306e\u3088\u3046\u306a\u51fa\u529b\u306b\u306a\u308b\u306f\u305a\u3067\u3059\u3002<\/p>\n\n\n\n
    $ .\/a.out\n101845628       0.191489\n123506854       0.720588\n139808122       0.433735\n141260304       0.723077\n14677762        0.623188\n150332786       0.582278\n150598871       0.575\n150622200       0.671642\n150794865       0.594937\n22667272        0.469136\n3348    1\n57619841        0.196721\n57619845        0.186992\n57619846        0.196721\n67722853        0.525\n67767321        0.551282\n68320883        0.487805\n71141694        0.896552\n9936344 0.769231<\/code><\/pre>\n\n\n\n
    \u7d9a\u304d\u306f\u5f8c\u7de8\u3067<\/h2>\n\n\n\n
    \u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u89e3\u8aac\u306a\u3069\u306f\u5f8c\u7de8<\/a>\u3067\u3084\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
    <\/p>\n","protected":false},"excerpt":{"rendered":"
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