{"id":1346,"date":"2021-08-29T14:39:51","date_gmt":"2021-08-29T05:39:51","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1346"},"modified":"2022-02-22T14:34:34","modified_gmt":"2022-02-22T05:34:34","slug":"openbabel%e3%81%a7%e5%88%86%e5%ad%90%e6%a7%8b%e9%80%a0%e3%81%ae%e3%82%a8%e3%83%8d%e3%83%ab%e3%82%ae%e3%83%bc%e6%a5%b5%e5%b0%8f%e5%8c%96","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2021\/08\/29\/openbabel%e3%81%a7%e5%88%86%e5%ad%90%e6%a7%8b%e9%80%a0%e3%81%ae%e3%82%a8%e3%83%8d%e3%83%ab%e3%82%ae%e3%83%bc%e6%a5%b5%e5%b0%8f%e5%8c%96\/","title":{"rendered":"OpenBabel\u3067\u5206\u5b50\u69cb\u9020\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316"},"content":{"rendered":"\n

\u8ad6\u6587\u66f8\u3044\u3066\u3044\u305f\u305f\u3081\u3001\u306a\u304b\u306a\u304b\u30d6\u30ed\u30b0\u306e\u66f4\u65b0\u3057\u3066\u3044\u306a\u304b\u3063\u305f\u306e\u3067\u3059\u304c\u3001\u4e45\u3005\u306bOpenBabel\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u30cd\u30bf\u306e\u30d6\u30ed\u30b0\u3092\u6295\u7a3f\u3057\u3066\u3044\u3053\u3046\u3068\u601d\u3044\u307e\u3059\u3002\u4eca\u56de\u306fOpenBabel\u306e\u5206\u5b50\u529b\u5834\u3092\u5229\u7528\u3057\u305f\u8a08\u7b97\u3092\u30c6\u30fc\u30de\u306b\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n\n\n\n\n

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

\u5206\u5b50\u529b\u5834\u3068\u8a00\u3048\u3070\u30b1\u30e2\u30a4\u30f3\u30d5\u30a9\u30de\u30c6\u30a3\u30af\u30b9\u306e\u8d85\u91cd\u8981\u306a\u30c6\u30fc\u30de\u304b\u3068\u601d\u3044\u307e\u3059\u3002\u5206\u5b50\u306e\u4e09\u6b21\u5143\u69cb\u9020\u3092\u767a\u751f\u3055\u305b\u308b\u305f\u3081\u306b\u306f\u5fc5\u305a\u5206\u5b50\u529b\u5834\u304c\u5fc5\u8981\u3067\u3059\u3057\u3001\u5404\u7a2e\u30a8\u30cd\u30eb\u30ae\u30fc\u3092\u8a55\u4fa1\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u306e\u3067\u3001\u8272\u3005\u306a\u89e3\u6790\u306b\u5fdc\u7528\u3067\u304d\u307e\u3059\u3002\u5148\u305a\u306f\u5206\u5b50\u69cb\u9020\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3059\u308bC++\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u7d39\u4ecb\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\u30d7\u30ed\u30b0\u30e9\u30e0<\/h2>\n\n\n\n

\u3058\u3064\u306fOpenBabel\u306b\u306f\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u306e\u30b3\u30de\u30f3\u30c9\u304c\u6a19\u6e96\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u307e\u3059\u3002\u305d\u306e\u30b3\u30de\u30f3\u30c9\u540d\u306f”obminimize”\u3067\u3059\u3002\u3053\u3053\u3067\u7d39\u4ecb\u3059\u308bC++\u30d7\u30ed\u30b0\u30e9\u30e0\u306f\u305d\u306e”obminimize”\u30b3\u30de\u30f3\u30c9\u306e\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u3092\u53ef\u80fd\u306a\u9650\u308a\u30b7\u30f3\u30d7\u30eb\u306b\u3057\u305f\u3088\u3046\u306a\u3082\u306e\u3068\u306a\u308a\u307e\u3059\u3002\u8a08\u7b97\u3057\u3066\u3044\u308b\u5185\u5bb9\u306f2\u6b21\u5143\u306e\u30a2\u30e9\u30ad\u30c9\u30f3\u9178\u306e\u69cb\u9020\u3092\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3057\u3066\u7c21\u6613\u7684\u306b3\u6b21\u5143\u3059\u308b\u3068\u3044\u3046\u3082\u306e\u3067\u3059\u3002<\/p>\n\n\n\n

\"\"
\u30a2\u30e9\u30ad\u30c9\u30f3\u9178\u306e2\u6b21\u5143\u69cb\u9020<\/figcaption><\/figure><\/div>\n\n\n\n

\u89e3\u8aac\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\u3068\u30c7\u30fc\u30bf\u3092\u307e\u3068\u3081\u305fZIP\u30d5\u30a1\u30a4\u30eb\u3092\u3053\u3053<\/a>\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304f\u3060\u3055\u3044\u3002C++\u30b3\u30fc\u30c9\u306e\u5185\u5bb9\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n

 1 #include <fstream>\n 2 #include <iostream>\n 3 #include <string>\n 4 \n 5 #include <openbabel\/mol.h>\n 6 #include <openbabel\/obconversion.h>\n 7 #include <openbabel\/forcefield.h>\n 8 \n 9 using namespace std;\n10 using namespace OpenBabel;\n11 \n12 int main(int argc, char* argv[]) {\n13   \/\/ \u529b\u5834\u306e\u8a2d\u5b9a\n14   string ff = \"MMFF94\";\n15   OBForceField* pFF = OBForceField::FindForceField(ff);\n16   if (!pFF) {\n17     cerr << \"\u6307\u5b9a\u306e\u529b\u5834\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n18     return -1;\n19   }\n20   pFF->SetLogFile(&cout);\n21   pFF->SetLogLevel(OBFF_LOGLVL_LOW);\n22 \n23   \/\/ \u30d5\u30a1\u30a4\u30eb\u30aa\u30fc\u30d7\u30f3\n24   ifstream ifs(\"Arachidonic_Acid.sdf\");\n25   if (ifs.fail()) {\n26     cerr << \"\u30d5\u30a1\u30a4\u30eb\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n27     return -1;\n28   }\n29 \n30   \/\/ \u53c2\u7167\u5206\u5b50\u306e\u8aad\u307f\u8fbc\u307f\n31   OBConversion conv;\n32   conv.SetInAndOutFormats(\"SDF\", \"SDF\");\n33   OBMol mol;\n34   conv.Read(&mol, &ifs);\n35   ifs.close();\n36 \n37   mol.AddHydrogens();  \/\/ \u6c34\u7d20\u4ed8\u52a0\n38 \n39   \/\/ \u5206\u5b50\u3092\u30bb\u30c3\u30c8\u30a2\u30c3\u30d7\uff08\u90e8\u5206\u96fb\u8377\u306a\u3069\u306e\u8a08\u7b97\uff09\n40   if (!pFF->Setup(mol)) {\n41     cerr << \"\u5206\u5b50\u306e\u8a2d\u5b9a\u306b\u5931\u6557\u3057\u307e\u3057\u305f\" << endl;\n42     return -1;\n43   }\n44 \n45   \/\/ \u6700\u6025\u964d\u4e0b\u6cd5\u304b\u3089\u306e\u5171\u5f79\u52fe\u914d\u6cd5\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\n46   pFF->SteepestDescent(5000, 1e-1);\n47   pFF->GetCoordinates(mol);\n48   pFF->ConjugateGradients(5000);\n49   pFF->GetCoordinates(mol);\n50 \n51   \/\/ \u5206\u5b50\u3092\u51fa\u529b\n52   ofstream ofs(\"Out_Arachidonic_Acid.sdf\");\n53   conv.Write(&mol, &ofs);\n54   ofs.close();\n55 \n56   return 0;\n57 }<\/code><\/pre>\n\n\n\n
\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u30b3\u30f3\u30d1\u30a4\u30eb\u3067\u304d\u307e\u3059\u3002\u306a\u304a\u3001Anaconda\u3092\u5229\u7528\u3057\u3066OpenBabel3\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u3042\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002\u3053\u308c\u306b\u3064\u3044\u3066\u306f\u4ee5\u524d\u306e\u30d6\u30ed\u30b0<\/a>\u3092\u53c2\u7167\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n
g++ -std=c++11 Minimize.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
\u30b3\u30fc\u30c9\u306e\u89e3\u8aac<\/h2>\n\n\n\n
\u5206\u5b50\u529b\u5834\u3092\u5229\u7528\u3059\u308b\u306b\u3042\u305f\u308a\u3001include\u3059\u3079\u304d\u306f7\u884c\u76ee\u306e””\u3067\u3059\u3002\u305d\u3057\u3066\u5206\u5b50\u529b\u5834\u306e\u5229\u7528\u958b\u59cb\u6642\u306bOBForceField\u30af\u30e9\u30b9\u306e\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9\u3092\u4f5c\u6210\u3057\u307e\u3059\u3002\u3053\u306e\u51e6\u7406\u306f15\u884c\u76ee\u3067\u884c\u3063\u3066\u3044\u307e\u3059\u3002FindForceField\u3068\u3044\u3046\u30e1\u30bd\u30c3\u30c9\u3092\u5229\u7528\u3059\u308b\u3053\u3068\u306b\u3088\u308aOpenBabel\u3067\u5206\u5b50\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u30bb\u30c3\u30c8\u3092\u6307\u5b9a\u3057\u3066OBForceFiled\u30af\u30e9\u30b9\u306e\u30a4\u30f3\u30b9\u30bf\u30f3\u30b9\u304c\u751f\u6210\u3055\u308c\u307e\u3059\u300214\u884c\u76ee\u3067ff = \"MMFF94\"<\/code>\u3068\u3057\u3066\u3044\u308b\u306e\u3067\u3001MMFF94\u3068\u3044\u3046\u5206\u5b50\u529b\u5834\uff08\u4f4e\u5206\u5b50\u306e\u8a08\u7b97\u3067\u306f\u826f\u304f\u5229\u7528\u3055\u308c\u307e\u3059\uff09\u3092\u5229\u7528\u3059\u308b\u4f8b\u3068\u306a\u308a\u307e\u3059\u3002
<\/p>\n\n\n\n
\u3061\u306a\u307f\u306bOpenBabel\u3067\u30b5\u30dd\u30fc\u30c8\u3055\u308c\u3066\u3044\u308b\u30d1\u30e9\u30e1\u30fc\u30bf\u30bb\u30c3\u30c8\u306f\u4ee5\u4e0b\u306e\u8868\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
\u529b\u5834\u540d<\/th>\u8aac\u660e<\/th><\/tr><\/thead>
GAFF<\/td>General Amber Force Field (GAFF).<\/td><\/tr>
Ghemical<\/td>Ghemical force field.<\/td><\/tr>
MMFF94<\/td>MMFF94 force field.<\/td><\/tr>
MMFF94s<\/td>MMFF94s force field.<\/td><\/tr>
UFF<\/td>Universal Force Field.<\/td><\/tr><\/tbody><\/table>
OpenBabel\u3067\u5229\u7528\u3067\u304d\u308b\u529b\u5834\u30d1\u30e9\u30e1\u30fc\u30bf\u4e00\u89a7<\/figcaption><\/figure>\n\n\n\n
20\u300121\u884c\u76ee\u3067\u306fOpenBabel\u304b\u3089\u51fa\u529b\u3055\u308c\u308b\u30ed\u30b0\u306e\u8a2d\u5b9a\u3092\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u3053\u3067\u306f\u30ed\u30b0\u306e\u51fa\u529b\u5148\u3092\u6a19\u6e96\u51fa\u529b\u306b\u3057\u3066\u3001\u30ed\u30b0\u306e\u51fa\u529b\u91cf\u3092LOW\u306b\u8a2d\u5b9a\u3057\u3066\u307e\u3059\u3002OBFF_LOGLVL_NONE<\/code>\u3092\u8a2d\u5b9a\u3059\u308b\u3068\u30ed\u30b0\u304c\u51fa\u529b\u3055\u308c\u306a\u304f\u306a\u308a\u307e\u3059\u3002\u7d9a\u3044\u306637\u884c\u76ee\u3067\u306f\u5206\u5b50\u306b\u6c34\u7d20\u539f\u5b50\u3092\u4ed8\u52a0\u3057\u3066\u3044\u307e\u3059\u300240\u884c\u76ee\u3067\u306f\u5206\u5b50\u3092\u30bb\u30c3\u30c8\u30a2\u30c3\u30d7\u3092\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u306e\u51e6\u7406\u3067\u5206\u5b50\u4e2d\u306e\u5404\u539f\u5b50\u306e\u5206\u5b50\u30bf\u30a4\u30d7\u3084\u90e8\u5206\u96fb\u8377\u3092\u30a2\u30b5\u30a4\u30f3\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u3053\u306e\u30d6\u30ed\u30b0\u306e\u4e3b\u984c\u306e\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u306f46\uff5e49\u884c\u76ee\u3067\u51e6\u7406\u3092\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002OpenBabel\u3067\u30b5\u30dd\u30fc\u30c8\u3057\u3066\u3044\u308b\u6700\u9069\u5316\u65b9\u6cd5\u306f\u6700\u6025\u964d\u4e0b\u6cd5\u3068\u5171\u5f79\u52fe\u914d\u6cd5\u3067\u3059\u3002\u305d\u308c\u305e\u308c\u306e\u7279\u5fb4\u3067\u3059\u304c\u6700\u9069\u5316\u65b9\u6cd5\u306f\u53ce\u675f\u306f\u9045\u3044\u304c\u9811\u5065\u3067\u3001\u8a08\u7b97\u9014\u4e2d\u3067\u30a8\u30cd\u30eb\u30ae\u30fc\u304c\u767a\u6563\u3059\u308b\u306a\u3069\u7834\u7dbb\u3059\u308b\u3053\u3068\u306f\u7a00\u3067\u3059\u3002\u4e00\u65b9\u3001\u5171\u5f79\u52fe\u914d\u6cd5\u306f\u53ce\u675f\u306f\u65e9\u3044\u304c\u6642\u3005\u8a08\u7b97\u304c\u7834\u7dbb\u3059\u308b\u3053\u3068\u304c\u3042\u308a\u307e\u3059\u3002\u4f4e\u5206\u5b50\u306e\u8a08\u7b97\u3067\u7834\u7dbb\u3057\u305f\u7d4c\u9a13\u306f\u6709\u308a\u307e\u305b\u3093\u304c\u3001\u300c\u30bf\u30f3\u30d1\u30af\u8cea+\u5927\u91cf\u306e\u6c34\u5206\u5b50\u300d\u306a\u3069\u306e\u5927\u304d\u306a\u7cfb\u3067\u306f\u3044\u304d\u306a\u308a\u5171\u5f79\u52fe\u914d\u6cd5\u3092\u9069\u7528\u3059\u308b\u3068\u7834\u7dbb\u3059\u308b\u3053\u3068\u304c\u3042\u308a\u307e\u3059\u3002\u591a\u5206\u3001\u5171\u5f79\u52fe\u914d\u6cd5\u306f\u30a8\u30cd\u30eb\u30ae\u30fc\u66f2\u9762\u3092\u4e8c\u6b21\u5f62\u5f0f\u3067\u8fd1\u4f3c\u3059\u308b\u3053\u3068\u3092\u524d\u63d0\u306b\u3057\u3066\u3044\u308b\u3053\u3068\u304c\u539f\u56e0\u304b\u306a\u3041\u3068\u601d\u3063\u3066\u3044\u307e\u3059\u3002\u3064\u307e\u308a\u6700\u6025\u964d\u4e0b\u6cd5\u3067\u3042\u308b\u7a0b\u5ea6\u6700\u9069\u5316\u3057\u3066\u3001\u30a8\u30cd\u30eb\u30ae\u30fc\u66f2\u9762\u304c\u4e8c\u6b21\u5f62\u5f0f\u3067\u8fd1\u4f3c\u3057\u3066\u3082\u5927\u4e08\u592b\u306a\u611f\u3058\u306b\u307e\u3067\u306a\u3063\u305f\u3089\u5171\u5f79\u52fe\u914d\u6cd5\u3092\u4f7f\u3046\u3068\u826f\u3044\u3067\u3057\u3087\u3046\u3002\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u306f\u6700\u6025\u964d\u4e0b\u6cd5\u304b\u3089\u306e\u5171\u5f79\u5f79\u52fe\u914d\u6cd5\u3067\u6700\u9069\u5316\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u6700\u5f8c\u306b52\uff5e54\u884c\u76ee\u3067\u69cb\u9020\u6700\u9069\u5316\u3057\u305f\u5206\u5b50\u3092\u30d5\u30a1\u30a4\u30eb\u306b\u51fa\u529b\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u8a08\u7b97\u7d50\u679c<\/h2>\n\n\n\n
\u6700\u5f8c\u306b\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3057\u305f\u30a2\u30e9\u30ad\u30c9\u30f3\u9178\u306e\u69cb\u9020\u3092\u4ee5\u4e0b\u306b\u56f3\u793a\u3057\u307e\u3059\u30022\u6b21\u5143\u69cb\u9020\u3092\u305d\u306e\u307e\u307e\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3057\u305f\u3060\u3051\u306a\u306e\u3067\u3042\u307e\u308a\u5909\u5316\u3092\u611f\u3058\u306a\u3044\u3067\u3059\u304c\u3001\u78ba\u304b\u306b3\u6b21\u5143\u69cb\u9020\u306b\u306a\u3063\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\"\"
OpenBabel\u3067minimize\u3057\u305f\u30a2\u30e9\u30ad\u30c9\u30f3\u9178\u306e\u69cb\u9020<\/figcaption><\/figure>\n","protected":false},"excerpt":{"rendered":"
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