{"id":1830,"date":"2021-12-24T10:10:00","date_gmt":"2021-12-24T01:10:00","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=1830"},"modified":"2022-02-22T14:28:30","modified_gmt":"2022-02-22T05:28:30","slug":"superpose_molecules_3","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2021\/12\/24\/superpose_molecules_3\/","title":{"rendered":"\u5206\u5b50\u306e\u6bcd\u6838\u69cb\u9020\u306e\u91cd\u306d\u5408\u308f\u305b\u3000\u5f8c\u7de8"},"content":{"rendered":"\n

\u4e2d\u7de8\u3067\u7d39\u4ecb\u3057\u305f\u5206\u5b50\u306e\u91cd\u306d\u5408\u308f\u305b\u306e\u8a08\u7b97\u65b9\u6cd5\u3092\u5b9f\u969b\u306bC++\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u7d44\u3093\u3067\u307f\u307e\u3059\u3002OpenBabel\u306e\u6a5f\u80fd\u3084\u5fdc\u7528\u3068\u8a00\u3046\u3088\u308a\u304b\u306f\u7dda\u578b\u4ee3\u6570\u306e\u8a08\u7b97\u304c\u30e1\u30a4\u30f3\u306a\u306e\u3067\u3001C++\u3067\u884c\u5217\u3092\u6271\u3046\u65b9\u6cd5\u306b\u3064\u3044\u3066\u3082\u8a00\u53ca\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n\n\n\n\n

\u8a08\u7b97\u5bfe\u8c61<\/h2>\n\n\n\n

\u4eca\u56de\u306e\u8a08\u7b97\u4f8b\u306f\u9069\u5f53\u306b3\u6b21\u5143\u5316\u3057\u305f\u30c9\u30cd\u30da\u30b8\u30eb\u3092\u3001PDB\u306e\u5171\u7d50\u6676\u69cb\u9020(6O4W)\u306b\u3042\u308b\u30c9\u30cd\u30da\u30b8\u30eb\u306b\u91cd\u306d\u308b\u8a08\u7b97\u3092\u3057\u307e\u3059\u3002\u30a4\u30e1\u30fc\u30b8\u3068\u3057\u3066\u306f\u4e0b\u56f3\u306e\u3088\u3046\u306a\u611f\u3058\u3067\u3059\u3002\u3053\u306e\u3068\u304d\u91cd\u306d\u308b\u6bcd\u6838\u306f\u30a4\u30f3\u30c0\u30ce\u30f3\u3092\u6307\u5b9a\u3059\u308b\u3053\u3068\u3068\u3057\u307e\u3059\u3002\u6a59\u8272\u306e\u5206\u5b50\u304c\u52d5\u304b\u3059\u65b9\u306e\u5206\u5b50\u3067\u3001\u7070\u8272\u306e\u5206\u5b50\u304c\u7d50\u6676\u69cb\u9020\u306e\u53c2\u7167\u3059\u308b\u5206\u5b50\u3067\u3059\u3002<\/p>\n\n\n\n

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

\u9069\u5f53\u306b\u767a\u751f\u3055\u305b\u305f\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u306a\u306e\u3067\u7d50\u6676\u69cb\u9020\u306b\u91cd\u306d\u5408\u308f\u305b\u308b\u3068\u3001\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30a2\u30df\u30ce\u9178\u5074\u9396\u306a\u3069\u306b\u885d\u7a81\u3059\u308b\u53ef\u80fd\u6027\u304c\u3042\u308a\u307e\u3059\u3002\u3057\u304b\u3057\u306a\u304c\u3089\u4eca\u56de\u306e\u76ee\u7684\u306f\u91cd\u306d\u308b\u3053\u3068\u306b\u4e3b\u773c\u3092\u7f6e\u304d\u3001\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u306e\u76f8\u4e92\u4f5c\u7528\u306a\u3069\u306f\u4eca\u56de\u306f\u8003\u616e\u3057\u306a\u3044\u3053\u3068\u3068\u3057\u3066\u3001\u3053\u308c\u3089\u306f\u5f8c\u306e\u30d6\u30ed\u30b0\u3067\u53d6\u308a\u6271\u3046\u3053\u3068\u3068\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

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

\u4eca\u56de\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3068\u30c7\u30fc\u30bf\u3092\u307e\u3068\u3081\u305fZIP\u30d5\u30a1\u30a4\u30eb\u306f\u3053\u3053\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n

MolSuperposition<\/a>\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/a><\/div>\n\n\n\n


\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u5b9f\u884c\u65b9\u6cd5\u3067\u3059\u304c\u3001\u5148\u305a\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3057\u3066Eigen<\/strong>\u3068\u3044\u3046\u30e9\u30a4\u30d6\u30e9\u30ea\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u304f\u3060\u3055\u3044\u3002Ubuntu\u306e\u5834\u5408\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u3001<\/p>\n\n\n\n

$ sudo apt install -y libeigen3-dev<\/code><\/pre>\n\n\n\n
CentOS\u306e\u5834\u5408\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u3059\u3002<\/p>\n\n\n\n
$ sudo yum -y install eigen3-devel<\/code><\/pre>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u30b3\u30f3\u30d1\u30a4\u30eb\u65b9\u6cd5\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
$ g++ -std=c++11 MolSuperposition.cpp \\\n      -I${HOME}\/anaconda3\/envs\/ob3\/include\/openbabel3 \\\n      -I\/usr\/include\/eigen3 \\\n      -L${HOME}\/anaconda3\/envs\/ob3\/lib \\\n      -Wl,-rpath=${HOME}\/anaconda3\/envs\/ob3\/lib -l openbabel<\/code><\/pre>\n\n\n\n
a.out<\/code>\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u304c\u51fa\u6765\u3066\u3044\u308c\u3070\u6210\u529f\u3067\u3059\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u5b9f\u884c\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u3059\u3002<\/p>\n\n\n\n
$ .\/a.out<\/code><\/pre>\n\n\n\n
\u3053\u306e\u30d6\u30ed\u30b0\u3067\u6271\u3046\u30d7\u30ed\u30b0\u30e9\u30e0\u304c\u3060\u3093\u3060\u3093\u9577\u304f\u306a\u3063\u3066\u304d\u3066\u5168\u90e8\u3092\u63b2\u8f09\u51fa\u6765\u306a\u304f\u306a\u3063\u3066\u304d\u307e\u3057\u305f\u3002C++\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u30b3\u30fc\u30c9\u30922\u3064\u306b\u5206\u5272\u3057\u3066\u89e3\u8aac\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002\u5148\u305a\u306f\u524d\u534a\u306e\u90e8\u5206\u3092\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 #include <openbabel\/parsmart.h>\n  9 #include <openbabel\/generic.h>\n 10 \n 11 #include <Eigen\/Dense>\n 12 \n 13 using namespace std;\n 14 using namespace OpenBabel;\n 15 using namespace Eigen;\n 16 \n 17 bool Superpose(OBMol& mol, OBMol& ref, string smarts);\n 18 \n 19 int main(int argc, char* argv[]) {\n 20   \/\/ \u529b\u5834\u306e\u8a2d\u5b9a\n 21   string ff = \"MMFF94\";\n 22   OBForceField* pFF = OBForceField::FindForceField(ff);\n 23   if (!pFF) {\n 24     cerr << \"\u6307\u5b9a\u306e\u529b\u5834\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n 25     return -1;\n 26   }\n 27   pFF->SetLogFile(&cout);\n 28   pFF->SetLogLevel(OBFF_LOGLVL_NONE);\n 29 \n 30   \/\/ \u30d5\u30a1\u30a4\u30eb\u30aa\u30fc\u30d7\u30f3\n 31   ifstream ifs1(\"Donepezil.sdf\");\n 32   if (ifs1.fail()) {\n 33     cerr << \"\u30d5\u30a1\u30a4\u30eb\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n 34     return -1;\n 35   }\n 36 \n 37   ifstream ifs2(\"template.sdf\");\n 38   if (ifs2.fail()) {\n 39     cerr << \"\u30d5\u30a1\u30a4\u30eb\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093\u3067\u3057\u305f\" << endl;\n 40     return -1;\n 41   }\n 42 \n 43   \/\/ \u53c2\u7167\u5206\u5b50\u306e\u8aad\u307f\u8fbc\u307f\n 44   OBConversion conv;\n 45   conv.SetInAndOutFormats(\"SDF\", \"SDF\");\n 46   OBMol mol, ref;\n 47   conv.Read(&mol, &ifs1);\n 48   conv.Read(&ref, &ifs2);\n 49   ifs1.close();\n 50   ifs2.close();\n 51 \n 52   \/\/ 2\u5206\u5b50\u306e\u91cd\u306d\u5408\u308f\u305b\u8a08\u7b97\n 53   Superpose(mol, ref, \"O=C1CCc2c1cccc2\");\n 54 \n 55   ofstream ofs(\"out.sdf\");\n 56   conv.Write(&mol, &ofs);\n 57   ofs.close();\n 58 \n 59   return 0;\n 60 }<\/code><\/pre>\n\n\n\n
\u5148\u305a\u7dda\u578b\u4ee3\u6570\u306e\u8a08\u7b97\u3092\u3059\u308b\u305f\u3081\u306b\u300111\u884c\u76ee\u306b#include <Eigen\/Dense><\/code>\u3068\u8a18\u8ff0\u3057\u3066\u3044\u307e\u3059\u3002\u3053\u308c\u306fEigen(https:\/\/eigen.tuxfamily.org\/index.php?title=Main_Page)\u3068\u3044\u3046C++\u7528\u306e\u7dda\u578b\u4ee3\u6570\u30e9\u30a4\u30d6\u30e9\u30ea\u3067\u3059\u3002\u7dda\u578b\u4ee3\u6570\u7528\u306e\u30e9\u30a4\u30d6\u30e9\u30ea\u3067\u6709\u540d\u306a\u3082\u306e\u306f\u3084\u306f\u308aLAPACK\/BLAS\u3067\u3057\u3087\u3046\u3002\u3053\u306eLAPACK\/BLAS\u306f\u4f55\u51e6\u306e\u30b9\u30fc\u30d1\u30fc\u30b3\u30f3\u30d4\u30e5\u30fc\u30bf\u306b\u3082\u6700\u9069\u5316\u3055\u308c\u305f\u3082\u306e\u304c\u5fc5\u305a\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u305f\u3060\u3001\u5143\u3005FORTRAN\u7528\u306b\u4f5c\u6210\u3055\u308c\u305f\u3082\u306e\u3067\u3001C++\u3067\u306e\u4f7f\u3044\u52dd\u624b\u306f\u30a4\u30de\u30a4\u30c1\u3067\u3001\u53e4\u81ed\u3044\u611f\u3058\u3067\u3059\u3002\u30b9\u30fc\u30d1\u30fc\u30b3\u30f3\u30d4\u30e5\u30fc\u30bf\u3067\u52d5\u304b\u3059\u30d7\u30ed\u30b0\u30e9\u30e0\u306fLAPACK\/BLAS\u3092\u5229\u7528\u3059\u3079\u304d\u306a\u306e\u3067\u3057\u3087\u3046\u304c\u3001Eigen\u306f\u975e\u5e38\u306b\u4f7f\u3044\u3084\u3059\u304f\u51fa\u6765\u3066\u3044\u3066\u3001\u79c1\u306f\u826f\u304f\u5229\u7528\u3057\u307e\u3059\u3002\u3053\u306e\u8a18\u4e8b\u3067\u306fEigen\u306e\u8a73\u3057\u3044\u4f7f\u3044\u65b9\u306b\u306f\u8a00\u53ca\u3057\u307e\u305b\u3093\u304c\u3001\u3044\u3064\u304b\u7d39\u4ecb\u3067\u304d\u308c\u3070\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
31\u884c\u76ee\u3067\u52d5\u304b\u3059\u65b9\u306e\u5206\u5b50\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u958b\u3044\u3066\u304a\u308a\u300137\u884c\u76ee\u3067\u306f\u53c2\u7167\u5206\u5b50\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u958b\u3044\u3066\u3044\u307e\u3059\u300253\u884c\u76ee\u3067\u5206\u5b50\u306e\u91cd\u306d\u5408\u308f\u305b\u8a08\u7b97\u3092\u3059\u308b\u95a2\u6570\u3092\u547c\u3073\u51fa\u3057\u3066\u3044\u308b\u306e\u3067\u3059\u304c\u3001\u4eca\u56de\u306e\u30d6\u30ed\u30b0\u306e\u30c6\u30fc\u30de\u306f\u5168\u3066\u3053\u306e\u95a2\u6570\u306b\u8a70\u3081\u8fbc\u3093\u3067\u3044\u307e\u3059\u3002
\u305d\u308c\u3067\u306f\u5f8c\u534a\u90e8\u5206\u3092\u898b\u3066\u3044\u304d\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n
 62 bool Superpose(OBMol& mol, OBMol& ref, string smarts) {\n 63   \/\/ \u6bcd\u6838\u69cb\u9020\u306e\u30de\u30c3\u30c1\u30f3\u30b0\n 64   OBSmartsPattern smp;\n 65   smp.Init(smarts);\n 66   smp.Match(mol);\n 67   vector<vector<int> > ml_mol = smp.GetUMapList();\n 68   smp.Match(ref);\n 69   vector<vector<int> > ml_ref = smp.GetUMapList();\n 70 \n 71   \/\/ \u6bcd\u6838\u4e2d\u5fc3\u5ea7\u6a19\u306e\u8a08\u7b97\n 72   Vector3d cm = Vector3d::Zero(3);\n 73   Vector3d cr = Vector3d::Zero(3);\n 74   for (int i = 0; i < ml_mol[0].size(); i++) {\n 75     OBAtom* a_mol = mol.GetAtom(ml_mol[0][i]);\n 76     cm(0) += a_mol->x();\n 77     cm(1) += a_mol->y();\n 78     cm(2) += a_mol->z();\n 79     OBAtom* a_ref = ref.GetAtom(ml_ref[0][i]);\n 80     cr(0) += a_ref->x();\n 81     cr(1) += a_ref->y();\n 82     cr(2) += a_ref->z();\n 83   }\n 84   cm \/= (double)(ml_mol[0].size());\n 85   cr \/= (double)(ml_mol[0].size());\n 86 \n 87   \/\/ 2\u5206\u5b50\u306e\u6bcd\u6838\u4e2d\u5fc3\u3092\u539f\u70b9\u3078\u79fb\u52d5\n 88   for (auto ii = mol.BeginAtoms(); ii != mol.EndAtoms(); ii++) {\n 89     double x = (*ii)->x() - cm(0);\n 90     double y = (*ii)->y() - cm(1);\n 91     double z = (*ii)->z() - cm(2);\n 92     (*ii)->SetVector(x, y, z);\n 93   }\n 94   for (auto ii = ref.BeginAtoms(); ii != ref.EndAtoms(); ii++) {\n 95     double x = (*ii)->x() - cr(0);\n 96     double y = (*ii)->y() - cr(1);\n 97     double z = (*ii)->z() - cr(2);\n 98     (*ii)->SetVector(x, y, z);\n 99   }\n100 \n101   \/\/ \u884c\u5217\u306e\u8a08\u7b97\n102   MatrixXd M = MatrixXd::Zero(4, 4);\n103   for (int i = 0; i < ml_mol[0].size(); i++) {\n104     OBAtom* a_mol = mol.GetAtom(ml_mol[0][i]);\n105     double x = a_mol->x();\n106     double y = a_mol->y();\n107     double z = a_mol->z();\n108     OBAtom* a_ref = ref.GetAtom(ml_ref[0][i]);\n109     double x0 = a_ref->x();\n110     double y0 = a_ref->y();\n111     double z0 = a_ref->z();\n112     M(0, 0) += -x * x0 - y * y0 - z * z0;\n113     M(1, 0) += z * y0 - y * z0;\n114     M(1, 1) += -x * x0 + y * y0 + z * z0;\n115     M(2, 0) += x * z0 - z * x0;\n116     M(2, 1) += -x * y0 - y * x0;\n117     M(2, 2) += x * x0 - y * y0 + z * z0;\n118     M(3, 0) += y * x0 - x * y0;\n119     M(3, 1) += -x * z0 - z * x0;\n120     M(3, 2) += -y * z0 - z * y0;\n121     M(3, 3) += x * x0 + y * y0 - z * z0;\n122   }\n123 \n124   \/\/ \u884c\u5217\u306e\u5bfe\u89d2\u5316\n125   SelfAdjointEigenSolver<MatrixXd> es(M);\n126   if (es.info() != Success) exit(0);\n127   VectorXd E;\n128   MatrixXd V;\n129   E = es.eigenvalues();\n130   V = es.eigenvectors();\n131 \n132   \/\/ \u56db\u5143\u6570\u304b\u3089\u56de\u8ee2\u884c\u5217\u3092\u8a08\u7b97\n133   Matrix3d R;\n134   double q0 = V(0, 0);\n135   double q1 = V(1, 0);\n136   double q2 = V(2, 0);\n137   double q3 = V(3, 0);\n138   R(0, 0) = q0 * q0 + q1 * q1 - q2 * q2 - q3 * q3;\n139   R(1, 0) = 2 * (q0 * q3 + q1 * q2);\n140   R(2, 0) = 2 * (q1 * q3 - q0 * q2);\n141   R(0, 1) = 2 * (q1 * q2 - q0 * q3);\n142   R(1, 1) = q0 * q0 - q1 * q1 + q2 * q2 - q3 * q3;\n143   R(2, 1) = 2 * (q2 * q3 + q0 * q1);\n144   R(0, 2) = 2 * (q0 * q2 + q1 * q3);\n145   R(1, 2) = 2 * (-q0 * q1 + q2 * q3);\n146   R(2, 2) = q0 * q0 - q1 * q1 - q2 * q2 + q3 * q3;\n147 \n148   \/\/ \u5206\u5b50\u306e\u56de\u8ee2\u3068\u4e26\u9032\n149   for (auto ii = mol.BeginAtoms(); ii != mol.EndAtoms(); ii++) {\n150     Vector3d X;\n151     X(0) = (*ii)->x();\n152     X(1) = (*ii)->y();\n153     X(2) = (*ii)->z();\n154     X = R * X;   \/\/ \u56de\u8ee2\n155     X = X + cr;  \/\/ \u4e26\u9032\n156     (*ii)->SetVector(X(0), X(1), X(2));\n157   }\n158 \n159   return true;\n160 }<\/code><\/pre>\n\n\n\n
\u5148\u305a\u3001\u5206\u5b50\u306e\u6bcd\u6838\u90e8\u5206\u3092\u7279\u5b9a\u3059\u308b\u305f\u3081\u306b63\uff5e69\u884c\u76ee\u3067\u90e8\u5206\u69cb\u9020\u691c\u7d22\u3092\u884c\u3063\u3066\u539f\u5b50\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u3092\u53d6\u5f97\u3057\u3066\u3044\u307e\u3059\u3002\u52d5\u304b\u3059\u65b9\u306e\u5206\u5b50\u306e\u539f\u5b50\u30ea\u30b9\u30c8\u306fml_mol<\/code>\u3068\u3044\u3046\u5909\u6570\u3067\u3001\u53c2\u7167\u5206\u5b50\u306e\u65b9\u306e\u539f\u5b50\u30ea\u30b9\u30c8\u306fml_ref<\/code>\u3068\u3044\u3046\u5909\u6570\u306b\u5165\u308c\u3066\u3044\u307e\u3059\u3002\u3069\u3061\u3089\u30821\u901a\u308a\u3057\u304b\u30d2\u30c3\u30c8\u3057\u306a\u3044\u3053\u3068\u304c\u5206\u304b\u3063\u3066\u3044\u308b\u306e\u3067\u3001ml_mol[0]<\/code>\u306e\u307f\u53c2\u7167\u3059\u308c\u3070\u826f\u3044\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002\u5206\u5b50\u306e\u91cd\u306d\u5408\u308f\u305b\u306e\u8a08\u7b97\u306f\u3001\u56de\u8ee2\u3059\u308b\u524d\u306b\u4e00\u65e6\u539f\u70b9\u3078\u56de\u8ee2\u4e2d\u5fc3\u3092\u79fb\u52d5\u3055\u305b\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002\u4e0a\u8a18\u30d7\u30ed\u30b0\u30e9\u30e0\u306e71\uff5e99\u884c\u76ee\u306f\u305d\u306e\u539f\u70b9\u3078\u306e\u79fb\u52d5\u3092\u884c\u3063\u3066\u3044\u307e\u3059\u3002101\uff5e122\u884c\u76ee\u3067\u306f\u5206\u5b50\u3092\u91cd\u306d\u308b\u56de\u8ee2\u3092\u8868\u3059\u56db\u5143\u6570\u3092\u6c42\u3081\u308b\u305f\u3081\u306e\\(4 \\times 4\\)\u884c\u5217\u3092\u8a08\u7b97\u3057\u3066\u3044\u307e\u3059\u3002124\uff5e130\u884c\u76ee\u3067\u306f\u884c\u5217\u3092\u5bfe\u89d2\u5316\u3057\u3066\u56fa\u6709\u5024\u3068\u56fa\u6709\u30d9\u30af\u30c8\u30eb\u3092\u8a08\u7b97\u3057\u3066\u3044\u307e\u3059\u3002\u4eca\u56de\u306f\u56fa\u6709\u5024\u306f\u4f7f\u3063\u3066\u3044\u306a\u3044\u306e\u3067129\u884c\u76ee\u306f\u7121\u304f\u3066\u3082\u3088\u3044\u3067\u3059\u3002132\uff5e146\u884c\u76ee\u3067\u306f\u56db\u5143\u6570\\(q=q_{0}+q_{1}i+q_{2}j+q_{3}k\\)\u304b\u3089\u56de\u8ee2\u884c\u5217\u3092\u69cb\u6210\u3057\u3066\u3044\u307e\u3059\u3002\u6700\u5f8c\u306b148\uff5e157\u884c\u76ee\u3067\u306f\u5206\u5b50\u3092\u56de\u8ee2\u3055\u305b\u3066\u3001\u53c2\u7167\u5206\u5b50\u306e\u4f4d\u7f6e\u3078\u79fb\u52d5\u3055\u305b\u3066\u3044\u307e\u3059\u3002\u5b9f\u306fEigen\u3068\u3044\u3046\u30e9\u30a4\u30d6\u30e9\u30ea\u306b\u306f\u56db\u5143\u6570\u3092\u6271\u3048\u308bQuaterniond<\/code>\u3068\u3044\u3046\u30af\u30e9\u30b9\u304c\u63d0\u4f9b\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u3053\u306e\u30af\u30e9\u30b9\u3092\u5229\u7528\u3059\u308c\u3070\u3001132\uff5e146\u884c\u76ee\u3067\u884c\u3063\u3066\u3044\u308b\u3088\u3046\u306a3\u6b21\u5143\u306e\u56de\u8ee2\u884c\u5217\u306e\u8a08\u7b97\u306f\u5fc5\u8981\u3042\u308a\u307e\u305b\u3093\u3002\u3053\u306eQuaterniond<\/code>\u30af\u30e9\u30b9\u3092\u5229\u7528\u3059\u308b\u5834\u5408\u306f132\uff5e157\u884c\u76ee\u3092\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u66f8\u304d\u63db\u3048\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n
  Quaterniond Q(V(0, 0),V(1, 0),V(2, 0),V(3, 0));\n  Matrix3d R=Q.toRotationMatrix();\n\n  \/\/ \u5206\u5b50\u306e\u56de\u8ee2\u3068\u79fb\u52d5\n  for (auto ii = mol.BeginAtoms(); ii != mol.EndAtoms(); ii++) {\n    Vector3d X;\n    X(0) = (*ii)->x();\n    X(1) = (*ii)->y();\n    X(2) = (*ii)->z();\n    X = Q * X;\n    X = X + cr;\n    (*ii)->SetVector(X(0), X(1), X(2));\n  }<\/code><\/pre>\n\n\n\n
\u8a08\u7b97\u7d50\u679c<\/h2>\n\n\n\n
\u4e0a\u8a18\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u5b9f\u884c\u3059\u308b\u3068out.sdf<\/code>\u3068\u3044\u3046SD\u30d5\u30a1\u30a4\u30eb\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u7d50\u6676\u69cb\u9020(PDBID:6O4W)\u3068\u51fa\u529b\u3055\u308c\u305fSD\u30d5\u30a1\u30a4\u30eb\u3092\u91cd\u306d\u5408\u308f\u305b\u305f\u56f3\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3059\u3002\u6bcd\u6838\u3068\u3057\u3066\u8a2d\u5b9a\u3057\u305f\u30a4\u30f3\u30c0\u30ce\u30f3\u90e8\u5206\u304c\u30d4\u30c3\u30bf\u30ea\u3068\u91cd\u306a\u3063\u3066\u3044\u308b\u3053\u3068\u304c\u5206\u304b\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
\"\"
\u5206\u5b50\u3092\u91cd\u306d\u305f\u7d50\u679c<\/figcaption><\/figure><\/div>\n\n\n\n
\u5076\u7136\u3067\u3057\u3087\u3046\u304c\u3001\u898b\u305f\u611f\u3058\u91cd\u306d\u305f\u5206\u5b50\u306f\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u306f\u3076\u3064\u304b\u3063\u3066\u3044\u306a\u3044\u3088\u3046\u306b\u898b\u3048\u307e\u3059\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
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