{"id":726,"date":"2019-10-11T13:30:20","date_gmt":"2019-10-11T04:30:20","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=726"},"modified":"2022-06-29T16:19:06","modified_gmt":"2022-06-29T07:19:06","slug":"openbabel_c_programming_beginner_search_2","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2019\/10\/11\/openbabel_c_programming_beginner_search_2\/","title":{"rendered":"OpenBabel\u3067C++\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u3000\uff5e\u8d85\u5165\u9580\u3000\u305d\u306e\uff12\uff5e"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">\u4eca\u56de\u306fSD\u30d5\u30a1\u30a4\u30eb<\/h2>\n\n\n\n<p style=\"text-align:left\">\u3000\u4eca\u56de\u306fSD\u30d5\u30a1\u30a4\u30eb\u3092\u53d6\u308a\u6271\u3063\u3066\u307f\u307e\u3059\u3002SD\u30d5\u30a1\u30a4\u30eb\u3068\u306f\u5316\u5408\u7269\u69cb\u9020\u3068\u305d\u308c\u306b\u4ed8\u968f\u3059\u308b\u69d8\u3005\u306a\u60c5\u5831\u3092\u53d6\u308a\u6271\u3046\u30d5\u30a1\u30a4\u30eb\u5f62\u5f0f\u3068\u3057\u3066\u5e83\u304f\u4f7f\u308f\u308c\u3066\u3044\u307e\u3059\u3002\u69cb\u9020\u5f0f\u3092\u8a18\u8ff0\u3059\u308b\u90e8\u5206\u306e\u5f62\u5f0f\u306fMOL\u5f62\u5f0f\u3068\u540c\u3058\u3067\u3001\u8907\u6570\u306e\u5206\u5b50\u3092\u53d6\u308a\u6271\u3048\u308b\u3053\u3068\u3084\u69d8\u3005\u306a\u60c5\u5831\u3092\u53d6\u308a\u6271\u3048\u308b\u3088\u3046\u306b\u4ed5\u69d8\u304c\u62e1\u5f35\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u3088\u308a\u8a73\u3057\u3044\u60c5\u5831\u306f\u4ee5\u4e0b\u306eweb\u30b5\u30a4\u30c8\u3092\u78ba\u8a8d\u3057\u3066\u307f\u3066\u4e0b\u3055\u3044\u3002<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/en.wikipedia.org\/wiki\/Chemical_table_file\">Wikipedia<\/a><\/li><li><a href=\"https:\/\/docs.chemaxon.com\/display\/docs\/Molecule+Formats\">ChemAxon<\/a><\/li><\/ul>\n\n\n\n<p>\u3000OpenBabel\u3067SD\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u66f8\u304d\u3059\u308b\u306b\u306f<strong>OBConversion<\/strong>\u30af\u30e9\u30b9\u306e<strong>SetInFormat<\/strong>\u30e1\u30bd\u30c3\u30c9\u3067&#8221;SDF&#8221;\u3092\u6307\u5b9a\u3059\u308c\u3070\u826f\u3044\u3060\u3051\u3067\u3059\u3002SD\u5f62\u5f0f\u304cMOL\u5f62\u5f0f\u3084SMILES\u3068\u7570\u306a\u308b\u306e\u306f\u8272\u3005\u306a\u30d7\u30ed\u30d1\u30c6\u30a3\uff08\u60c5\u5831\uff09\u304c\u5165\u3063\u3066\u3044\u308b\u70b9\u3067\u3001\u3053\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u6271\u308f\u306a\u3044\u3068SD\u5f62\u5f0f\u3092\u5229\u7528\u3059\u308b\u610f\u5473\u304c\u3042\u308a\u307e\u305b\u3093\u3002\u3057\u305f\u304c\u3063\u3066\u3001SD\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u6271\u3046\u65b9\u6cd5\u3092\u7d39\u4ecb\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<!--more-->\n\n\n\n<h2 class=\"wp-block-heading\">PubChem\u306eSD\u30d5\u30a1\u30a4\u30eb<\/h2>\n\n\n\n<p>\u3000<a href=\"https:\/\/pubchem.ncbi.nlm.nih.gov\/\">PubChem<\/a>\u304b\u3089\u4f8b\u3068\u3057\u3066\u6271\u3048\u308bSD\u30d5\u30a1\u30a4\u30eb\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u7528\u610f\u3057\u3066\u307f\u307e\u3057\u305f\u3002\u30d5\u30a1\u30a4\u30eb\u306e\u4e2d\u8eab\u3092\u5c11\u3057\u898b\u3066\u307f\u308b\u3068\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u307e\u3059\u3002&#8221;\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9&#8221;\u3092\u30af\u30ea\u30c3\u30af\u3057\u3066SD\u30d5\u30a1\u30a4\u30eb\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u307f\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n<div class=\"wp-block-file\"><a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2019\/09\/EGFR_lig.sdf\">EGFR_lig.sdf<\/a><a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2019\/09\/EGFR_lig.sdf\" class=\"wp-block-file__button\" download>\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/a><\/div>\n\n\n\n<pre class=\"wp-block-code\"><code>9549299\n  -OEChem-07121920292D\n\n 48 51  0     0  0  0  0  0  0999 V2000\n    2.3660   -1.2010    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0000   -2.5670    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n    3.3660   -2.9330    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0\n   12.3923    2.4330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   11.5263    0.9330    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n...\n...\n 28 47  1  0  0  0  0\n 30 48  1  0  0  0  0\nM  END\n&gt; &lt;PUBCHEM_COMPOUND_CID&gt;\n9549299\n\n&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;\n1\n\n&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;\n586\n\n...\n...<\/code><\/pre>\n\n\n\n<p>\u3000\u6700\u521d\u304b\u3089&#8221;M END&#8221;\u307e\u3067\u304c\u69cb\u9020\u5f0f\u306e\u60c5\u5831\u3067\u3001MOL\u5f62\u5f0f\u3068\u540c\u3058\u3067\u3059\u3002\u305d\u3053\u304b\u3089\u4e0b\u306e&#8221;&gt; &lt;PUBCHEM_COMPOUND_CID&gt;&#8221;\u304c\u30d7\u30ed\u30d1\u30c6\u30a3\u306e\u30bf\u30a4\u30c8\u30eb\u3067\u3001\u305d\u308c\u306b\u5bfe\u5fdc\u3059\u308b\u5185\u5bb9\u304c\u76f4\u4e0b\u306b\u8a18\u8ff0\u3055\u308c\u3066\u3044\u308b&#8221;9549299&#8243;\u3068\u306a\u308a\u307e\u3059\u3002\u305d\u3057\u3066\u3053\u306eSD\u30d5\u30a1\u30a4\u30eb\u306b\u306f11\u500b\u306e\u5206\u5b50\u306e\u60c5\u5831\u304c\u8a18\u8ff0\u3055\u308c\u3066\u304a\u308a\u30011\u5206\u5b50\u6bce\u306b\u3001\u60c5\u5831\u306e\u7d42\u308f\u308a\u3068\u3057\u3066\u5fc5\u305a&#8221;$$$$&#8221;\u3068\u3044\u3046\u8a18\u53f7\u3067\u7d42\u4e86\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<p>\u3000\u5148\u305aSD\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e&#8221;PUBCHEM_MOLECULAR_WEIGHT&#8221;\u3068&#8221;PUBCHEM_XLOGP3_AA&#8221;\u3068\u3044\u30462\u500b\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\uff08\u5206\u5b50\u91cf\u3068logP\uff09\u3092\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u8aad\u307f\u53d6\u3063\u3066\u307f\u307e\u3057\u3087\u3046\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u306f&#8221;<a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2019\/09\/readSDF1.cpp\">readSDF1.cpp<\/a>&#8220;\u3067\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>  1 #include &lt;iostream&gt;\n  2 #include &lt;fstream&gt;\n  3 #include &lt;string&gt;\n  4 \n  5 #include &lt;openbabel\/mol.h&gt;\n  6 #include &lt;openbabel\/obconversion.h&gt;\n  7 \n  8 using namespace std;\n  9 using namespace OpenBabel;\n 10 \n 11 int main(int argc, char* argv[]) {\n 12   ifstream ifs(\"EGFR_lig.sdf\");\n 13 \n 14   OBConversion conv;\n 15   conv.SetInFormat(\"SDF\");\n 16 \n 17   OBMol mol;\n 18   vector&lt;OBMol&gt; lib;\n 19   while (conv.Read(&amp;mol, &amp;ifs)) {\n 20     lib.push_back(mol);\n 21   }\n 22   ifs.close();\n 23 \n 24   for (auto ii = lib.begin(); ii != lib.end(); ii++) {\n 25     string s_MW = ii-&gt;GetData(\"PUBCHEM_MOLECULAR_WEIGHT\")-&gt;GetValue();\n 26     double MW = stof(s_MW);\n 27     string s_logP = ii-&gt;GetData(\"PUBCHEM_XLOGP3_AA\")-&gt;GetValue();\n 28     double logP = stof(s_logP);\n 29     cout &lt;&lt; ii-&gt;GetTitle() &lt;&lt; \"\\t\" &lt;&lt; MW &lt;&lt; \"\\t\" &lt;&lt; logP &lt;&lt; endl;\n 30   }\n 31 }<\/code><\/pre>\n\n\n\n<p>\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u30b3\u30f3\u30d1\u30a4\u30eb\u3057\u307e\u3059<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>g++ -std=c++11 readSDF1.cpp -I\/home\/username\/app\/include\/openbabel-2.0 -L\/home\/username\/app\/lib -lopenbabel<\/code><\/pre>\n\n\n\n<p>\u3000\u30dd\u30a4\u30f3\u30c8\u306f25\u884c\u76ee\u306827\u884c\u76ee\u306e&#8221;GetData&#8221;\u30e1\u30bd\u30c3\u30c9\u3067\u3059\u3002\u3053\u3053\u306e\u5f15\u6570\u306b\u53d6\u5f97\u3057\u305f\u3044\u30d7\u30ed\u30d1\u30c6\u30a3\u540d\u3092\u6307\u5b9a\u3057\u307e\u3059\u3002\u305d\u3057\u3066&#8221;GetValue()&#8221;\u3067\u305d\u306e\u5024\u304c\u6587\u5b57\u5217\u3068\u306a\u3063\u3066\u53d6\u5f97\u3067\u304d\u307e\u3059\u3002\u53d6\u5f97\u3059\u308b\u5909\u6570\u306e\u578b\u306f\u6587\u5b57\u5217\u306a\u306e\u3067\u3001\u5206\u5b50\u91cf\u306e\u3088\u3046\u306a\u5b9f\u6570\u306e\u5834\u5408\u306f&#8221;stof&#8221;\u95a2\u6570\u3067\u5b9f\u6570\u5316\u3057\u307e\u3059\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u5b9f\u884c\u3059\u308b\u3068\u4ee5\u4e0b\u306e\u3088\u3046\u306a\u51fa\u529b\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>9549299 413.4   4.5\n78358313        445.6   3.3\n9843206 387.4   4.8\n6711154 365.3   4\n11566580        355.8   3.6\n132117821       490     3.1\n127264586       490     3.1\n118797290       397.6   4.6\n126496758       487.5   3.4\n129627019       436.5   4.7\n91668194        415.4   1.2<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u30d7\u30ed\u30d1\u30c6\u30a3\u306e\u4f5c\u6210\u3068\u524a\u9664<\/h2>\n\n\n\n<p>\u3000\u6b21\u306f\u72ec\u81ea\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u8ffd\u52a0\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\u3042\u3068\u3001\u3064\u3044\u3067\u306b\u4f55\u304b1\u3064\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u524a\u9664\u3082\u3057\u3066\u307f\u307e\u3059\u3002\u3068\u308a\u3042\u3048\u305a\u30d7\u30ed\u30b0\u30e9\u30e0&#8221;<a href=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2019\/09\/readSDF2.cpp\">readSDF2.cpp<\/a>&#8220;\u3092\u3054\u89a7\u304f\u3060\u3055\u3044\u3002\u5c11\u3057\u30b3\u30fc\u30c9\u304c\u9577\u304f\u306a\u3063\u3066\u304d\u305f\u306e\u3067\u3001\u30dd\u30a4\u30f3\u30c8\u3068\u306a\u308b\u90e8\u5206\u3060\u3051\u8f09\u305b\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code> 24   conv.SetOutFormat(\"CAN\");\n 25   for (auto ii = lib.begin(); ii != lib.end(); ii++) {\n 26     \/\/ SMILES\u3092\u53d6\u5f97\u3059\u308b\n 27     string smiles = conv.WriteString(&amp;*ii);\n 28     smiles.erase(smiles.find('\\t'));\n 29 \n 30     \/\/ \u30d7\u30ed\u30d1\u30c6\u30a3\u3068\u3057\u3066SMILES\n 31     OBPairData* p = new OBPairData;\n 32     p-&gt;SetAttribute(\"OpenBabel_SMILES\");\n 33     p-&gt;SetValue(smiles);\n 34     ii-&gt;SetData(p);\n 35 \n 36     \/\/ \u30d7\u30ed\u30d1\u30c6\u30a3\u30921\u3064\u524a\u9664\u3059\u308b\n 37     ii-&gt;DeleteData(\"PUBCHEM_IUPAC_INCHI\");\n 38   }<\/code><\/pre>\n\n\n\n<p>\u3000\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u306fOpenBabel\u306e\u6a5f\u80fd\u3067\u69cb\u9020\u306eSMILES\u3092\u4f5c\u6210\u3057\u3066&#8221;OpenBabel_SMILES&#8221;\u3068\u3044\u3046\u65b0\u3057\u3044\u30d7\u30ed\u30d1\u30c6\u30a3\u540d\u3067\u305d\u306eSMILES\u3092SD\u30d5\u30a1\u30a4\u30eb\u306b\u8ffd\u52a0\u3057\u3066\u3044\u307e\u3059\u3002\u3042\u3068&#8221;PUBCHEM_IUPAC_INCHI&#8221;\u3068\u3044\u3046\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u524a\u9664\u3057\u3066\u3044\u307e\u3059\u3002&#8221;readSDF2.cpp&#8221;\u3092\u30b3\u30f3\u30d1\u30a4\u30eb\u3057\u3066\u30d7\u30ed\u30b0\u30e9\u30e0\u5b9f\u884c\u3059\u308b\u3068\u3001&#8221;New_EGFR_lig.sdf&#8221;\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u304c\u4f5c\u6210\u3055\u308c\u307e\u3059\u3002\u30a8\u30c7\u30a3\u30bf\u306a\u3069\u3067\u524d\u8ff0\u3057\u305f\u3088\u3046\u306a\u30d7\u30ed\u30d1\u30c6\u30a3\u304c\u51fa\u6765\u3066\u3044\u308b\u304b\u3069\u3046\u304b\u4e2d\u8eab\u3092\u78ba\u8a8d\u3057\u3066\u307f\u3066\u4e0b\u3055\u3044\u3002<\/p>\n\n\n\n<p 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