{"id":1031,"date":"2020-03-12T15:49:14","date_gmt":"2020-03-12T06:49:14","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1031"},"modified":"2022-06-29T16:22:23","modified_gmt":"2022-06-29T07:22:23","slug":"openbabel_c_programming_substructure_search_2","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2020\/03\/12\/openbabel_c_programming_substructure_search_2\/","title":{"rendered":"OpenBabel\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u90e8\u5206\u69cb\u9020\u691c\u7d22\u3000\u305d\u306e2\uff5e"},"content":{"rendered":"\n

\u3000\u524d\u56de\u306b\u5f15\u304d\u7d9a\u304d\u90e8\u5206\u69cb\u9020\u691c\u7d22\u30cd\u30bf\u3067\u3044\u304d\u307e\u3059\u3002\u4eca\u56de\u306f\u3082\u3046\u5c11\u3057\u5b9f\u7528\u7684\u306a\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u7d39\u4ecb\u3057\u307e\u3059\u3002\u305d\u308c\u306f\u533b\u85ac\u54c1\u3068\u3057\u3066\u671b\u307e\u3057\u304f\u306a\u3044\u90e8\u5206\u69cb\u9020\u3092\u6301\u3064\u5316\u5408\u7269\u3092\u30e9\u30a4\u30d6\u30e9\u30ea\u304b\u3089\u6392\u9664\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u3059\u3002\u65e5\u672c\u306b\u304a\u3044\u3066\u8cfc\u5165\u3067\u304d\u308b\u4f4e\u5206\u5b50\u5316\u5408\u7269\u306f1000\u4e07\u4ee5\u4e0a\u3042\u308b\u306e\u3067\u3059\u304c\u3001\u305d\u306e\u4e2d\u306b\u306f\u533b\u85ac\u54c1\u3068\u3057\u3066\u554f\u984c\u304c\u3042\u308a\u305d\u3046\u306a\uff08\u6bd2\u6027\u304c\u61f8\u5ff5\u3055\u308c\u308b\uff09\u69cb\u9020\u3092\u3082\u3064\u3082\u306e\u304c\u6ca2\u5c71\u3042\u308a\u307e\u3059\u3002\u5927\u62b5\u306f\u53cd\u5fdc\u6027\u304c\u9ad8\u304f\u3001\u6709\u6a5f\u5408\u6210\u306b\u5229\u7528\u3059\u308b\u53cd\u5fdc\u8a66\u85ac\u306a\u3069\u304c\u307b\u3068\u3093\u3069\u3067\u3059\u304c\u3001\u30a4\u30f3\u30b7\u30ea\u30b3\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u3092\u884c\u3046\u969b\u306f\u305d\u308c\u3089\u3092\u4e88\u3081\u6392\u9664\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002<\/p>\n\n\n\n\n\n\n\n

\u90e8\u5206\u69cb\u9020\u30d5\u30a3\u30eb\u30bf\u30fc<\/h2>\n\n\n\n

\u3000\u5275\u85ac\u306e\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u306b\u304a\u3044\u3066\u671b\u307e\u3057\u304f\u306a\u3044\u90e8\u5206\u69cb\u9020\u306e\u30ea\u30b9\u30c8\u3068\u3057\u3066\u6700\u3082\u6709\u540d\u306a\u306e\u306f\u4e0b\u56f3\u306e\u3082\u306e\u3067\u306f\u306a\u3044\u3067\u3057\u3087\u3046\u304b\u3002\u3053\u308c\u306fRishton\u306e\u8ad6\u6587<\/a>\u3067\u7d39\u4ecb\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u3053\u308c\u3060\u3051\u3067\u306a\u304f\u4ed6\u306b\u3082\u6392\u9664\u3059\u3079\u304d\u90e8\u5206\u69cb\u9020\u304c\u3042\u308b\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u304c\u3001\u3068\u308a\u3042\u3048\u305a\u4e0b\u56f3\u306e\u69cb\u9020\u3092\u6392\u9664\u3059\u308b\u7c21\u5358\u306a\u30d7\u30ed\u30b0\u30e9\u30e0\u304c”filter.cpp<\/a>“\u3067\u3059\u3002\u30ea\u30f3\u30af\u3092\u53f3\u30af\u30ea\u30c3\u30af\u3057\u3066\u30ea\u30f3\u30af\u5148\u3092\u4fdd\u5b58\u3057\u3066\u4e0b\u3055\u3044\u3002\u30b3\u30f3\u30d1\u30a4\u30eb\u306b\u3064\u3044\u3066\u306f\u4ee5\u524d\u304b\u3089\u307b\u3068\u3093\u3069\u540c\u3058\u30b3\u30de\u30f3\u30c9\u306a\u306e\u3067\u3001\u305d\u308d\u305d\u308d\u66f8\u304f\u306e\u304c\u9762\u5012\u306b\u306a\u3063\u3066\u304d\u307e\u3057\u305f\u304c\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u884c\u3044\u307e\u3059\u3002<\/p>\n\n\n\n

$ g++ -std=c++11 filter.cpp -I\/home\/username\/app\/include\/openbabel-2.0 -L\/home\/username\/app\/lib -lopenbabel<\/code><\/pre>\n\n\n\n
\"\"
\u671b\u307e\u3057\u304f\u306a\u3044\u5b98\u80fd\u57fa<\/figcaption><\/figure>\n\n\n\n
\u3000\u4f7f\u3044\u65b9\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u5165\u529b\u306eSD\u30d5\u30a1\u30a4\u30eb”input.sdf”\u3068\u51fa\u529b\u306eSD\u30d5\u30a1\u30a4\u30eb”output.sdf”\u3092\u5f15\u6570\u306b\u6307\u5b9a\u3057\u3066\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3057\u307e\u3059\u3002\u4e0a\u8a18\u306e\u69cb\u9020\u3092\u6392\u9664\u3057\u305f\u5f8c\u306e\u5316\u5408\u7269\u69cb\u9020\u304c”output.sdf”\u306b\u51fa\u529b\u3055\u308c\u307e\u3059\u3002<\/p>\n\n\n\n
$ .\/a.out input.sdf output.sdf<\/code><\/pre>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u5c11\u3057\u89e3\u8aac<\/h2>\n\n\n\n
\u3000\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u672c\u4f53\u306fFilter\u30af\u30e9\u30b9\u3067\u3059\u3002\u4ee5\u4e0b\u306e\u30b3\u30fc\u30c9\u306f\u3001\u3053\u306e\u30af\u30e9\u30b9\u306e\u90e8\u5206\u3060\u3051\u629c\u7c8b\u3057\u3066\u793a\u3057\u307e\u3059\u3002Filter\u30af\u30e9\u30b9\u306e\u30b3\u30f3\u30b9\u30c8\u30e9\u30af\u30bf\u3067\u6392\u9664\u3059\u3079\u304d\u90e8\u5206\u69cb\u9020\u306e\u521d\u671f\u5316\u3068\u8ffd\u52a0\u3092\u3072\u305f\u3059\u3089\u7e70\u308a\u8fd4\u3057\u3066\u3044\u307e\u3059\u3002\u8ffd\u52a0\u5148\u306fOBSmartsPattern\u306e\u30d9\u30af\u30bf\u30fc\u3068\u306a\u3063\u3066\u3044\u307e\u3059\u3002\u305d\u3057\u3066\u5316\u5408\u7269\u306e\u30c1\u30a7\u30c3\u30af\u306fCheck\u3068\u3044\u3046\u30e1\u30bd\u30c3\u30c9\u3067\u884c\u3063\u3066\u304a\u308a\u307e\u3059\u3002\u8a72\u5f53\u3059\u308b\u90e8\u5206\u69cb\u9020\u304c1\u500b\u3067\u3082\u30de\u30c3\u30c1\u3057\u305f\u5834\u5408\u306ffalse\u3092\u8fd4\u3057\u3066\u3001\u90e8\u5206\u69cb\u9020\u304c1\u500b\u3082\u30de\u30c3\u30c1\u3057\u306a\u3044\u5834\u5408\u306ftrue\u3092\u8fd4\u3059\u3088\u3046\u306b\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u3000\u3053\u306e\u30af\u30e9\u30b9\u306f\u96e3\u3057\u3044\u66f8\u304d\u65b9\u306b\u306f\u306a\u3063\u3066\u3044\u306a\u3044\u3068\u601d\u3044\u307e\u3059\u3002\u72ec\u81ea\u306e\u90e8\u5206\u69cb\u9020\u3092\u8ffd\u52a0\u3057\u305f\u3044\u5834\u5408\u306f\u3001sm.Init(“\u72ec\u81ea\u30d1\u30bf\u30fc\u30f3”); sms.push_back(sm);\u3068\u8ffd\u8a18\u3057\u3066\u4e0b\u3055\u3044\u3002\u554f\u984c\u306a\u306e\u306fSMARTS\u30d1\u30bf\u30fc\u30f3\u306e\u4f5c\u308a\u65b9\u3067\u3059\u3002\u3053\u308c\u306f\u8a66\u884c\u932f\u8aa4\u3057\u306a\u3044\u3068\u306a\u304b\u306a\u304b\u3046\u307e\u304f\u4f5c\u308c\u307e\u305b\u3093\u3002\u304b\u306a\u308a\u4f5c\u308a\u3053\u307e\u306a\u3044\u3068\u6392\u9664\u3057\u305f\u304f\u7121\u3044\u69cb\u9020\u3092\u6392\u9664\u3057\u3066\u3057\u307e\u3046\u3053\u3068\u306b\u306a\u308b\u3067\u3057\u3087\u3046\u3002\u4f8b\u3048\u3070\u9396\u72b6\u306e\u30a8\u30b9\u30c6\u30eb\u3092\u6392\u9664\u3057\u305f\u3044\u304c\u30e9\u30af\u30c8\u30f3\u306f\u6392\u9664\u3057\u305f\u304f\u306a\u3044\u5834\u5408\u306fSMARTS\u306e\u4e2d\u306b\u74b0\u69cb\u9020\u3067\u306f\u306a\u3044\u3068\u3044\u3046\u6761\u4ef6\u3092\u5165\u308c\u306a\u3051\u308c\u3070\u306a\u308a\u307e\u305b\u3093\u3002<\/p>\n\n\n\n
 13 class Filter {\n 14   vector<OBSmartsPattern> sms;\n 15\n 16  public:\n 17   Filter() {\n 18     OBSmartsPattern sm;\n 19\n 20     sm.Init(\"[F,Cl,Br,I]S(=O)(=O)*\");  \/\/ \u30cf\u30ed\u30b2\u30f3\u5316\u30b9\u30eb\u30db\u30cb\u30eb\n 21     sms.push_back(sm);\n 22\n 23     sm.Init(\"[F,Cl,Br,I]C(=O)*\");  \/\/ \u30cf\u30ed\u30b2\u30f3\u5316\u30a2\u30b7\u30eb\n 24     sms.push_back(sm);\n 25\n 26     sm.Init(\"[F,Cl,Br,I][CX4H2]*\");  \/\/ \u30cf\u30ed\u30b2\u30f3\u5316\u30a2\u30eb\u30ad\u30eb\n 27     sms.push_back(sm);\n 28\n 29     sm.Init(\"*C(=O)!@-O!@-C(=O)*\");  \/\/ \u9178\u7121\u6c34\u7269\n 30     sms.push_back(sm);\n 31\n 32     sm.Init(\"[F,Cl,Br,I]c1[nH0]ccc[nH0]1\");  \/\/ \u30cf\u30ed\u30b2\u30f3\u5316\u30d4\u30ea\u30df\u30b8\u30f3\n 33     sms.push_back(sm);\n 34\n 35     sm.Init(\"[CX3H1](=O)[#6]\");  \/\/ \u30a2\u30eb\u30c7\u30d2\u30c9\n 36     sms.push_back(sm);\n 37\n 38     sm.Init(\"*C(C*)=[NX2]*\");  \/\/ \u30a4\u30df\u30f3\n 39     sms.push_back(sm);\n 40\n 41     sm.Init(\"[F,Cl,Br,I]C([F,Cl,Br,I])([F,Cl,Br,I])C(=O)C*\");  \/\/ \u30d1\u30fc\u30cf\u30ed\u30b1\u30c8\u30f3\n 42     sms.push_back(sm);\n 43\n 44     sm.Init(\"[#6]O!@-C(=O)[#6]\");  \/\/ \u8102\u80aa\u65cf\u30a8\u30b9\u30c6\u30eb\n 45     sms.push_back(sm);\n 46\n 47     sm.Init(\"*C!@-C(=O)[CX4H3]\");  \/\/ \u8102\u80aa\u65cf\u30b1\u30c8\u30f3\n 48     sms.push_back(sm);\n 49\n 50     sm.Init(\"O1CC1\");  \/\/ \u30a8\u30dd\u30ad\u30b7\u30c9\n 51     sms.push_back(sm);\n 52\n 53     sm.Init(\"N1CC1\");  \/\/ \u30a2\u30b8\u30ea\u30b8\u30f3\n 54     sms.push_back(sm);\n 55\n 56     sm.Init(\"[#6]S!@-C(=O)[#6]\");  \/\/ \u30c1\u30aa\u30a8\u30b9\u30c6\u30eb\n 57     sms.push_back(sm);\n 58\n 59     sm.Init(\"[#6]O!@-S(=O)(=O)[#6]\");  \/\/ \u30b9\u30eb\u30db\u30f3\u9178\u30a8\u30b9\u30c6\u30eb\n 60     sms.push_back(sm);\n 61\n 62     sm.Init(\"[#6]O!@-P(=O)(-[OH])[#6]\");  \/\/ \u30db\u30b9\u30db\u30f3\u9178\u30a8\u30b9\u30c6\u30eb\n 63     sms.push_back(sm);\n 64\n 65     sm.Init(\"[F,Cl,Br,I][CX4H2]C(=O)*\");  \/\/ \u03b1-\u30cf\u30ed\u30ab\u30eb\u30dc\u30cb\u30eb\u5316\u5408\u7269\n 66     sms.push_back(sm);\n 67\n 68     sm.Init(\"O=C(*)!@-C(=O)*\");  \/\/ 1,2-\u30b8\u30ab\u30eb\u30dc\u30cb\u30eb\u5316\u5408\u7269\n 69     sms.push_back(sm);\n 70\n 71     sm.Init(\"*C[CH]!@=[CH]!@-C(*)=O\");  \/\/ \u30de\u30a4\u30b1\u30eb\u53d7\u5bb9\u4f53\n 72     sms.push_back(sm);\n 73\n 74     sm.Init(\"*C[CH]([F,Cl,Br,I])!@-[CH2]!@-C(*)=O\");  \/\/ \u03b2-\u30d8\u30c6\u30ed\u7f6e\u63db\u30ab\u30eb\u30dc\u30cb\u30eb\u5316\u5408\u7269\n 75     sms.push_back(sm);\n 76\n 77     sm.Init(\"*O!@-O*\");  \/\/ O-O\u7d50\u5408\n 78     sms.push_back(sm);\n 79\n 80     sm.Init(\"*N!@-O*\");  \/\/ N-O\u7d50\u5408\n 81     sms.push_back(sm);\n 82\n 83     sm.Init(\"*N!@-N*\");  \/\/ N-\u7d50\u5408\n 84     sms.push_back(sm);\n 85\n 86     sm.Init(\"*S!@-N*\");  \/\/ S-N\u7d50\u5408\n 87     sms.push_back(sm);\n 88\n 89     sm.Init(\"*S!@-S*\");  \/\/ S-S\u7d50\u5408\n 90     sms.push_back(sm);\n 91\n 92     sm.Init(\"*S!@-O*\");  \/\/ S-O\u7d50\u5408\n 93     sms.push_back(sm);\n 94   }\n 95\n 96   bool Check(OBMol& mol) {\n 97     for (auto ii = sms.begin(); ii != sms.end(); ii++) {\n 98       if (ii->Match(mol)) return false;\n 99     }\n100     return true;\n101   }\n102 };<\/code><\/pre>\n\n\n\n
\u5bbf\u984c<\/h2>\n\n\n\n
\u3000\u672c\u6765\u306a\u3089SMARTS\u306e\u30ea\u30b9\u30c8\u3092\u5916\u90e8\u30d5\u30a1\u30a4\u30eb\u3068\u3057\u3066\u4f5c\u6210\u3057\u3066\u3001\u30d7\u30ed\u30b0\u30e9\u30e0\u5b9f\u884c\u6642\u306b\u8aad\u307f\u8fbc\u307e\u305b\u308b\u3088\u3046\u306a\u4ed5\u69d8\u306b\u3059\u3079\u304d\u3067\u3059\u3002\u305d\u306e\u65b9\u304c\u8272\u3005\u3068\u5fdc\u7528\u304c\u52b9\u304f\u3057\u3001\u30d7\u30ed\u30b0\u30e9\u30e0\u81ea\u4f53\u3082\u30b9\u30c3\u30ad\u30ea\u3057\u307e\u3059\u3002\u4eca\u56de\u305d\u306e\u69d8\u306b\u3057\u306a\u304b\u3063\u305f\u306e\u306f\u5358\u7d14\u306b\u9762\u5012\u3060\u3063\u305f\u304b\u3089\u3067\u3059\u3002\u4f59\u529b\u304c\u3042\u308b\u65b9\u306f\u662f\u975e\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3092SMARTS\u30ea\u30b9\u30c8\u3092\u8aad\u307f\u8fbc\u307e\u305b\u308b\u69d8\u306b\u6539\u826f\u3057\u3066\u307f\u3066\u4e0b\u3055\u3044\u3002<\/p>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n\n\n\n
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