{"id":1372,"date":"2021-09-02T16:05:29","date_gmt":"2021-09-02T07:05:29","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1372"},"modified":"2022-02-22T14:32:03","modified_gmt":"2022-02-22T05:32:03","slug":"openbabel-conformation-search","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2021\/09\/02\/openbabel-conformation-search\/","title":{"rendered":"OpenBabel\u3067\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1"},"content":{"rendered":"\n

\u524d\u56de\u306b\u5f15\u304d\u7d9a\u304d\u5206\u5b50\u529b\u5834\u306e\u8a71\u984c\u306e\u7b2c\u4e8c\u5f3e\u3067\u3059\u3002\u4eca\u56de\u306f\u6700\u5b89\u5b9a\u69cb\u9020\u3092\u63a2\u7d22\u3057\u3066\u307f\u3088\u3046\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n\n\n\n\n

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

\u524d\u56de\u306e\u30d6\u30ed\u30b0<\/a>\u3067\u306f\u5358\u7d14\u306b\u30a8\u30cd\u30eb\u30ae\u30fc\u6975\u5c0f\u5316\u3059\u308b\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u7d39\u4ecb\u3057\u307e\u3057\u305f\u304c\u3001\u5b9f\u7528\u7684\u306a\u4e09\u6b21\u5143\u5206\u5b50\u69cb\u9020\u3092\u5f97\u308b\u306b\u306f\u3082\u3063\u3068\u30a8\u30cd\u30eb\u30ae\u30fc\u306e\u4f4e\u3044\u69cb\u9020\u3092\u63a2\u7d22\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002\u3053\u306e\u3088\u3046\u306a\u69cb\u9020\u63a2\u7d22\u306e\u3053\u3068\u3092\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1\u3068\u8a00\u308f\u308c\u307e\u3059\u3002OpenBabel\u306b\u306f\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1\u3092\u5b9f\u884c\u3059\u308b\u6a5f\u80fd\u3082\u4ed8\u3044\u3066\u3044\u308b\u306e\u3067\u3001\u3053\u308c\u3092\u8a66\u3057\u3066\u307f\u3088\u3046\u3068\u601d\u3044\u307e\u3059\u3002OpenBabel\u306eC++\u306eAPI\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8<\/a>\u3092\u898b\u3066\u307f\u308b\u3068\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1\u306e\u6a5f\u80fd\u3092\u63d0\u4f9b\u3059\u308b\u30e1\u30bd\u30c3\u30c9\u306f\u6b21\u306e\u8868\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n

\u30e1\u30bd\u30c3\u30c9\u540d<\/th>\u8aac\u660e<\/th><\/tr><\/thead>
SystematicRotorSearch<\/td>\u56de\u8ee2\u53ef\u80fd\u306a\u5168\u3066\u306e\u7d50\u5408\u3092\u56de\u8ee2\u3055\u305b\u308b\u3002\u7d44\u307f\u5408\u308f\u305b\u304c\u7206\u767a\u3057\u3066\u5b9f\u7528\u7684\u3067\u306f\u306a\u3044\u3002<\/td><\/tr>
RandomRotorSearch<\/td>\u30e9\u30f3\u30c0\u30e0\u306b\u9078\u629e\u3055\u308c\u305f\u7d50\u5408\u3092\u56de\u8ee2\u3055\u305b\u308b\u3002<\/td><\/tr>
WeightedRotorSearch<\/td>\u30a8\u30cd\u30eb\u30ae\u30fc\u3092\u4f4e\u304f\u3059\u308b\u3088\u3046\u306a\u7d50\u5408\u306e\u56de\u8ee2\u3092\u512a\u5148\u7684\u306b\u8a08\u7b97\u3059\u308b\u3002<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

\u3053\u3046\u3057\u3066\u898b\u3066\u307f\u308b\u3068”WeightedRotorSearch”\u304c\u4e00\u756a\u826f\u3044\u3088\u3046\u306b\u898b\u3048\u307e\u3059\u3002\u5b9f\u969b”obabel”\u30b3\u30de\u30f3\u30c9\u306e\u30aa\u30d7\u30b7\u30e7\u30f3\u3067”--gen3d best<\/code>“\u3068\u5165\u529b\u3059\u308b\u3068\u3053\u306e”WeightedRotorSearch”\u3092\u5229\u7528\u3057\u3066\u63a2\u7d22\u3057\u3066\u3044\u307e\u3059\u3002\u3068\u3044\u3046\u3053\u3068\u3067\u3001\u3053\u306e\u30d6\u30ed\u30b0\u3067\u8a66\u3057\u3066\u307f\u308b\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1\u306f”WeightedRotorSearch”\u3068\u3057\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n

\u30d7\u30ed\u30b0\u30e9\u30e0\u89e3\u8aac<\/h2>\n\n\n\n

\u3068\u308a\u3042\u3048\u305a\u3001\u4eca\u56de\u306e\u30d6\u30ed\u30b0\u306e\u30c6\u30fc\u30de\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u30b3\u30fc\u30c9\u3092\u4ee5\u4e0b\u306b\u793a\u3057\u307e\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   pFF->WeightedRotorSearch(250, 10);\n52   pFF->GetCoordinates(mol);\n53 \n54   \/\/ \u5206\u5b50\u3092\u51fa\u529b\n55   ofstream ofs(\"Out_Arachidonic_Acid.sdf\");\n56   conv.Write(&mol, &ofs);\n57   ofs.close();\n58 \n59   return 0;\n60 }<\/code><\/pre>\n\n\n\n
\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306f\u524d\u56de\u3068\u307b\u3068\u3093\u3069\u540c\u3058\u3067\u3059\u300251, 52\u884c\u76ee\u306b\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1\u3059\u308b”WeightedRotorSearch”\u30e1\u30bd\u30c3\u30c9\u3092\u5229\u7528\u3059\u308b\u8a18\u8ff0\u304c\u633f\u5165\u3055\u308c\u305f\u3060\u3051\u3067\u3059\u3002
\u5b9f\u306b\u7c21\u5358\u3067\u3059\u306d\u3002\u5b9f\u884c\u3057\u3066\u8a66\u3057\u305f\u3044\u5834\u5408\u306f\u3001\u524d\u56de\u306e\u30d6\u30ed\u30b0\u306e\u30d7\u30ed\u30b0\u30e9\u30e0<\/a>\u3092\u524d\u8ff0\u306e\u901a\u308a\u4fee\u6b63\u3057\u3066\u307f\u3066\u304f\u3060\u3055\u3044\u3002\u3061\u306a\u307f\u306b\u5f15\u6570\u306e250\u306810\u306fOpenBabel\u306e\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9(gen3d.cpp)\u306e174\u884c\u76ee\u306e\u8a18\u8ff0\u3092\u53c2\u8003\u306b\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
172     switch(speed) {\n173     case 1:\n174       pFF->WeightedRotorSearch(250, 10); \/\/ maybe based on # of rotatable bonds?\n175       break;\n176     case 2:\n177       pFF->FastRotorSearch(true); \/\/ permute central rotors\n178       break;\n179     case 3:\n180     default:\n181       pFF->FastRotorSearch(false); \/\/ only one permutation\n182     }<\/code><\/pre>\n\n\n\n
\u8a08\u7b97\u7d50\u679c<\/h2>\n\n\n\n
\u30a2\u30e9\u30ad\u30c9\u30f3\u9178\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u30b5\u30fc\u30c1\u3092\u5b9f\u884c\u3057\u3066\u307f\u305f\u7d50\u679c\u306e\u56f3\u3092\u4ee5\u4e0b\u306b\u793a\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
\"\"<\/figure><\/div>\n\n\n\n
\u524d\u56de\u8a08\u7b97\u3057\u305f\u7d50\u679c\u3068\u6bd4\u3079\u3066\u4e2d\u3005\u826f\u3044\u611f\u3058\u306e\u69cb\u9020\u306b\u306a\u3063\u305f\u306e\u3067\u306f\u306a\u3044\u304b\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u98fd\u548c\u74b0\u3092\u542b\u3080\u5834\u5408<\/h2>\n\n\n\n
\u4e0a\u8a18\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u7d50\u679c\u306f\u3001OpenBabel\u306e”--gen3d<\/code>“\u30aa\u30d7\u30b7\u30e7\u30f3\u30673\u6b21\u5143\u69cb\u9020\u3092\u7acb\u3061\u4e0a\u3052\u305f\u5834\u5408\u3068\u5927\u4f53\u540c\u3058\u7d50\u679c\u306b\u306a\u308b\u306e\u3067\u306f\u306a\u3044\u304b\u3068\u601d\u3044\u307e\u3059\u3002\u3067\u3001\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u98fd\u548c\u516d\u54e1\u74b0\u3092\u542b\u3080\u8a08\u7b97\u3092\u3059\u308b\u3068\u5c11\u3057\u6b8b\u5ff5\u306a\u69cb\u9020\u304c\u51fa\u529b\u3055\u308c\u308b\u5834\u5408\u304c\u3042\u308a\u307e\u3059\u3002\u4f8b\u3048\u3070\u30d4\u30da\u30ea\u30b8\u30f3\u74b0\u3092\u542b\u3093\u3067\u3044\u308b\u30c9\u30cd\u30da\u30b8\u30eb\uff08sdfile: Donepezil.sdf<\/a>\uff09\u3092\u4e0a\u8a18\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u4e09\u6b21\u5143\u5316\u3059\u308b\u3068\u3001\u4e0b\u56f3\u306e\u3088\u3046\u306b\u98fd\u548c\u516d\u54e1\u74b0\u304c\u306d\u3058\u308c\u821f\u578b\u306e\u69cb\u9020\u306b\u306a\u308a\u307e\u3057\u305f\u3002<\/p>\n\n\n\n
\"\"<\/figure><\/div>\n\n\n\n
\u98fd\u548c\u516d\u54e1\u74b0\u306f\u3044\u3059\u578b\u306b\u306a\u308b\u5834\u5408\u304c\u307b\u3068\u3093\u3069\u306e\u306f\u305a\u3067\u3059\u3002\u3053\u308c\u306f”WeightedRotorSearch”\u3067\u306f\u74b0\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u307e\u3067\u306f\u63a2\u7d22\u3057\u306a\u3044\u4e8b\u304c\u539f\u56e0\u304b\u3068\u601d\u308f\u308c\u307e\u3059\u3002\u3057\u304b\u3057\u306a\u304c\u3089\u3001OpenBabel\u306eAPI\u30c9\u30ad\u30e5\u30e1\u30f3\u30c8\u3092\u81ea\u5206\u3067\u30d3\u30eb\u30c9\u3057\u3066\u8aad\u3093\u3067\u307f\u308b\u3068\u3001\u30aa\u30d7\u30b7\u30e7\u30f31\u3064\u5165\u308c\u308b\u3060\u3051\u3067\u74b0\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3082\u63a2\u7d22\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u308b\u307f\u305f\u3044\u3067\u3059\u3002\u305d\u308c\u306f”WeightedRotorSearch”\u30e1\u30bd\u30c3\u30c9\u306e\u7b2c\u4e09\u5f15\u6570\u306b”true”\u3092\u5165\u308c\u308b\u3060\u3051\u3067\u3059\u3002\u3068\u3044\u3046\u3053\u3068\u3067\u30d7\u30ed\u30b0\u30e9\u30e0\u306e51\u884c\u76ee\u3092\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u5fae\u4fee\u6b63\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n
51   pFF->WeightedRotorSearch(250, 10, true);<\/code><\/pre>\n\n\n\n
\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u30c9\u30cd\u30da\u30b8\u30eb\u3092\u4e09\u6b21\u5143\u5316\u3059\u308b\u3068\u4e0b\u56f3\u306e\u3088\u3046\u306a\u3044\u3044\u611f\u3058\u306e\u30d4\u30da\u30ea\u30b8\u30f3\u69cb\u9020\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
\"\"<\/figure><\/div>\n","protected":false},"excerpt":{"rendered":"
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