{"id":2231,"date":"2020-02-26T14:19:32","date_gmt":"2020-02-26T05:19:32","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=2231"},"modified":"2025-08-06T12:54:11","modified_gmt":"2025-08-06T03:54:11","slug":"2231","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2020\/02\/26\/2231\/","title":{"rendered":"RDKit\u3092\u4f7f\u3063\u305f\u4f4e\u5206\u5b50\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u63a2\u7d22"},"content":{"rendered":"<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h1 id=\"RDKit\u306b\u3088\u308b\u4f4e\u5206\u5b50\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u63a2\u7d22\">RDKit\u306b\u3088\u308b\u4f4e\u5206\u5b50\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u63a2\u7d22<\/h1>\n<h2 id=\"ETKTG\u6cd5\u3092\u4f7f\u3063\u305f\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u751f\u6210\u3001\u30a8\u30cd\u30eb\u30ae\u30fc\u6700\u9069\u5316\">ETKTG\u6cd5\u3092\u4f7f\u3063\u305f\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u751f\u6210\u3001\u30a8\u30cd\u30eb\u30ae\u30fc\u6700\u9069\u5316<\/h2>\n<p>\u7814\u7a76\u5ba4\u5185\u7528\u306e\u30e1\u30e2\u3067\u3059\u3002Jupyter Lab\u5f62\u5f0f\u30d5\u30a1\u30a4\u30eb\uff08<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/sample.ipynb_.zip\">sample.ipynb<\/a>\uff09\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u81ea\u5206\u3067\u52d5\u304b\u3057\u3066\u307f\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n<p><strong>\u7d50\u8ad6\u3092\u5148\u306b\u66f8\u3044\u3066\u304a\u304f\u3068\u3001\u4eca\u56de\u306e\u65b9\u6cd5\u3067\u306f\u30c6\u30b9\u30c8\u5206\u5b50\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u306e\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0\u3092\u3046\u307e\u304f\u3067\u304d\u307e\u305b\u3093\u3067\u3057\u305f\u3002<\/strong><\/p>\n<p>\u4eca\u56de\u30c6\u30b9\u30c8\u3067\u4f7f\u7528\u3057\u305f9\u54e1\u74b0\u30e9\u30af\u30bf\u30e0\u5206\u5b50\uff08Indolactam-V\uff09\u3067\u306f\u30c8\u30e9\u30f3\u30b9\u30a2\u30df\u30c9\u578b\u304c\u307b\u307c\u751f\u6210\u3055\u308c\u305a\uff082000\u500b\u767a\u751f\u3055\u305b\u30661\u500b\u3060\u3051\uff09\u3001\u305d\u308c\u3082\u5b9f\u9a13\u7684\u306b\u5206\u304b\u3063\u3066\u3044\u308b\u5b89\u5b9a\u306a\u30c8\u30e9\u30f3\u30b9\u30a2\u30df\u30c9\u578b\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\uff08Sofa\u578b\uff09\u3067\u306f\u3042\u308a\u307e\u305b\u3093\u3067\u3057\u305f\u3002<a href=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/memo\/conformational-search\/\">\u4ee5\u524d\u7d39\u4ecb\u3057\u305fGROMACS\u306eSimulated Annealing\u3092\u4f7f\u3063\u305f\u65b9\u6cd5<\/a>\u3060\u3068\u30b7\u30b9\u30a2\u30df\u30c9\u578b\u3082\u30c8\u30e9\u30f3\u30b9\u30a2\u30df\u30c9\u578b\u3082\u6e80\u904d\u306a\u304f\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0\u3067\u304d\u3066\u3044\u308b\u306e\u3067\u305d\u3061\u3089\u3092\u4f7f\u3063\u305f\u65b9\u304c\u307e\u3060\u5b89\u5fc3\u306e\u3088\u3046\u3067\u3059\u3002<\/p>\n<p>\u4ee5\u4e0b\u306e\u30b5\u30a4\u30c8\u3092\u53c2\u8003\u306b\u3055\u305b\u3066\u3044\u305f\u3060\u304d\u307e\u3057\u305f:<\/p>\n<ul>\n<li><a href=\"https:\/\/www.rdkit.org\/docs_jp\/RDKit_cookbook_jp.html\">RDKit\u30af\u30c3\u30af\u30d6\u30c3\u30af &#8211; RDKit_unofficial_translation_JP 2019.03.1 \u30c9\u30ad\u30e5\u30e1\u30f3\u30c8<\/a><\/li>\n<li><a title=\"A workflow for docking\/virtual screening\" href=\"https:\/\/www.macinchem.org\/reviews\/docking\/docking.php\">A workflow for docking\/virtual screening &#8211; Macs in Chemistry<\/a><\/li>\n<li><a href=\"https:\/\/future-chem.com\/rdkit-conformer\/\">RDKit\u306b\u3088\u308b\u30b3\u30f3\u30d5\u30a9\u30de\u30fc\u306e\u751f\u6210 &#8211; \u5316\u5b66\u306e\u65b0\u3057\u3044\u30ab\u30bf\u30c1<\/a><\/li>\n<li><a href=\"https:\/\/iwatobipen.wordpress.com\/2012\/10\/21\/rdkit%E3%81%A7%E9%85%8D%E5%BA%A7%E3%82%92%E7%99%BA%E7%94%9F%E3%81%95%E3%81%9B%E3%81%A6%E3%82%A8%E3%83%8D%E3%83%AB%E3%82%AE%E3%83%BC%E3%82%92%E8%A8%88%E7%AE%97%E3%81%97%E3%81%A6%E3%81%BF%E3%82%8B\/\">RDKit\u3067\u914d\u5ea7\u3092\u767a\u751f\u3055\u305b\u3066\u30a8\u30cd\u30eb\u30ae\u30fc\u3092\u8a08\u7b97\u3057\u3066\u307f\u308b &#8211; IS LIFE WORTH LIVING?<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"Library\u306eImport\">Library\u306eImport<\/h3>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[1]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"kn\">import<\/span> <span class=\"nn\">os<\/span>\n\n<span class=\"kn\">import<\/span> <span class=\"nn\">numpy<\/span> <span class=\"k\">as<\/span> <span class=\"nn\">np<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"NumPy version:\"<\/span><span class=\"p\">,<\/span> <span class=\"n\">np<\/span><span class=\"o\">.<\/span><span class=\"n\">__version__<\/span><span class=\"p\">)<\/span>\n\n<span class=\"kn\">import<\/span> <span class=\"nn\">rdkit<\/span> <span class=\"c1\"># RDKit 2019.09.3<\/span>\n<span class=\"kn\">from<\/span> <span class=\"nn\">rdkit<\/span> <span class=\"kn\">import<\/span> <span class=\"n\">Chem<\/span> \n<span class=\"kn\">from<\/span> <span class=\"nn\">rdkit.Chem<\/span> <span class=\"kn\">import<\/span> <span class=\"n\">AllChem<\/span><span class=\"p\">,<\/span> <span class=\"n\">Draw<\/span><span class=\"p\">,<\/span> <span class=\"n\">Descriptors<\/span><span class=\"p\">,<\/span> <span class=\"n\">PandasTools<\/span><span class=\"p\">,<\/span> <span class=\"n\">TorsionFingerprints<\/span>\n<span class=\"kn\">from<\/span> <span class=\"nn\">rdkit.ML.Cluster<\/span> <span class=\"kn\">import<\/span> <span class=\"n\">Butina<\/span>\n<span class=\"kn\">from<\/span> <span class=\"nn\">rdkit.Chem.Draw<\/span> <span class=\"kn\">import<\/span> <span class=\"n\">IPythonConsole<\/span>\n<span class=\"c1\">#IPythonConsole.ipython_3d=True<\/span>\n\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"RDKit version:\"<\/span><span class=\"p\">,<\/span> <span class=\"n\">rdkit<\/span><span class=\"o\">.<\/span><span class=\"n\">__version__<\/span><span class=\"p\">)<\/span>\n\n<span class=\"kn\">import<\/span> <span class=\"nn\">nglview<\/span> <span class=\"c1\"># NGLView 2.7.1<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"NGLView version:\"<\/span><span class=\"p\">,<\/span> <span class=\"n\">nglview<\/span><span class=\"o\">.<\/span><span class=\"n\">__version__<\/span><span class=\"p\">)<\/span>\n\n<span class=\"kn\">import<\/span> <span class=\"nn\">pandas<\/span> <span class=\"k\">as<\/span> <span class=\"nn\">pd<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"Pandas version:\"<\/span><span class=\"p\">,<\/span> <span class=\"n\">pd<\/span><span class=\"o\">.<\/span><span class=\"n\">__version__<\/span><span class=\"p\">)<\/span>\n\n<span class=\"kn\">import<\/span> <span class=\"nn\">pubchempy<\/span> <span class=\"k\">as<\/span> <span class=\"nn\">pcp<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"PubChemPy version:\"<\/span><span class=\"p\">,<\/span> <span class=\"n\">pcp<\/span><span class=\"o\">.<\/span><span class=\"n\">__version__<\/span><span class=\"p\">)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>NumPy version: 1.18.1\n<\/pre>\n<\/div>\n<\/div>\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stderr output_text\">\n<pre>RDKit WARNING: [14:21:55] Enabling RDKit 2019.09.3 jupyter extensions\n<\/pre>\n<\/div>\n<\/div>\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>RDKit version: 2019.09.3\n<\/pre>\n<\/div>\n<\/div>\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div id=\"9c2fe623-da5a-4c30-b6e6-31d361fd68bb\">&nbsp;<\/div>\n<div class=\"output_subarea output_widget_view \"><script type=\"text\/javascript\"><br \/>\nvar element = $('#9c2fe623-da5a-4c30-b6e6-31d361fd68bb');<br \/>\n<\/script><br \/>\n<script type=\"application\/vnd.jupyter.widget-view+json\"><br \/>\n{\"model_id\": \"b5f7a8879e6946ca9b4b0d170c6b1999\", \"version_major\": 2, \"version_minor\": 0}<br \/>\n<\/script><\/div>\n<\/div>\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>NGLView version: 2.7.1\nPandas version: 1.0.1\nPubChemPy version: 1.0.4\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"SMILES-string\u306e\u8aad\u307f\u8fbc\u307f\">SMILES string\u306e\u8aad\u307f\u8fbc\u307f<\/h3>\n<p><a href=\"https:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/Aplysiatoxin\">Aplysiatoxin. Pubchem CID: 21672114.<\/a><br \/>\n<a href=\"https:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/105000\">Indolactam-V. Pubchem CID: 105000.<\/a><\/p>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[2]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">pubchemcid<\/span> <span class=\"o\">=<\/span> <span class=\"mi\">105000<\/span>\n<span class=\"n\">smiles<\/span> <span class=\"o\">=<\/span> <span class=\"n\">pcp<\/span><span class=\"o\">.<\/span><span class=\"n\">get_properties<\/span><span class=\"p\">(<\/span><span class=\"s1\">'IsomericSMILES'<\/span><span class=\"p\">,<\/span> <span class=\"n\">pubchemcid<\/span><span class=\"p\">)<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"n\">smiles<\/span><span class=\"p\">)<\/span>\n<span class=\"n\">mol<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Chem<\/span><span class=\"o\">.<\/span><span class=\"n\">MolFromSmiles<\/span><span class=\"p\">(<\/span><span class=\"n\">smiles<\/span><span class=\"p\">[<\/span><span class=\"mi\">0<\/span><span class=\"p\">][<\/span><span class=\"s1\">'IsomericSMILES'<\/span><span class=\"p\">])<\/span>\n<span class=\"n\">Draw<\/span><span class=\"o\">.<\/span><span class=\"n\">MolToImage<\/span><span class=\"p\">(<\/span><span class=\"n\">mol<\/span><span class=\"p\">)<\/span> <span class=\"c1\"># RDKit\u306b\u3088\u308b\u69cb\u9020\u306e\u8868\u793a<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>[{'CID': 105000, 'IsomericSMILES': 'CC(C)[C@H]1C(=O)N[C@@H](CC2=CNC3=C2C(=CC=C3)N1C)CO'}]\n<\/pre>\n<\/div>\n<\/div>\n<div class=\"output_area\">\n<div class=\"prompt output_prompt\">Out[2]:<\/div>\n<div class=\"output_png output_subarea output_execute_result\"><img decoding=\"async\" src=\"data:image\/png;base64,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\"><\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3092\u767a\u751f\u3059\u308b\u95a2\u6570\u3001\u30b3\u30f3\u30db\u30de\u30fc\u6570\u3092\u5b9a\u7fa9\u3059\u308b\">\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3092\u767a\u751f\u3059\u308b\u95a2\u6570\u3001\u30b3\u30f3\u30db\u30de\u30fc\u6570\u3092\u5b9a\u7fa9\u3059\u308b<\/h3>\n<p>ETKTG\u6cd5\u3092\u4f7f\u7528<\/p>\n<ul>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.5b00654\">Riniker, S.; Landrum, G. A. Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. <em>J. Chem. Inf. Model.<\/em> <strong>2015<\/strong>, <em>55<\/em>, 2562-2574<\/a>.<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[3]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">ps<\/span> <span class=\"o\">=<\/span> <span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">ETKDGv2<\/span><span class=\"p\">()<\/span> <span class=\"c1\"># AllChem.ETKDG() \u304c\u30c7\u30d5\u30a9\u30eb\u30c8<\/span>\n<span class=\"n\">ps<\/span><span class=\"o\">.<\/span><span class=\"n\">pruneRmsThresh<\/span> <span class=\"o\">=<\/span> <span class=\"mf\">0.2<\/span> <span class=\"c1\"># 0 \u3060\u3068\u679d\u5208\u308a\u3057\u306a\u3044<\/span>\n<span class=\"n\">ps<\/span><span class=\"o\">.<\/span><span class=\"n\">numThreads<\/span> <span class=\"o\">=<\/span> <span class=\"mi\">0<\/span> <span class=\"c1\">#\u4e26\u5217\u5b9f\u884c\u6570\u30020\u306f\u6700\u5927\u306e\u30b9\u30ec\u30c3\u30c9\u6570\u3092\u4f7f\u7528\u3002<\/span>\n<span class=\"c1\">#\u751f\u6210\u3059\u308b\u30b3\u30f3\u30db\u30de\u30fc\u6570; \u4f8b: n = 100<\/span>\n<span class=\"n\">n<\/span> <span class=\"o\">=<\/span> <span class=\"mi\">2000<\/span>\n\n<span class=\"k\">def<\/span> <span class=\"nf\">generateconformations<\/span><span class=\"p\">(<\/span><span class=\"n\">m<\/span><span class=\"p\">,<\/span> <span class=\"n\">n<\/span><span class=\"p\">):<\/span>\n    <span class=\"n\">m_h<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Chem<\/span><span class=\"o\">.<\/span><span class=\"n\">AddHs<\/span><span class=\"p\">(<\/span><span class=\"n\">m<\/span><span class=\"p\">)<\/span> <span class=\"c1\">#\u6c34\u7d20\u539f\u5b50\u306e\u4ed8\u52a0<\/span>\n    <span class=\"n\">ids<\/span> <span class=\"o\">=<\/span> <span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">EmbedMultipleConfs<\/span><span class=\"p\">(<\/span><span class=\"n\">m_h<\/span><span class=\"p\">,<\/span> <span class=\"n\">n<\/span><span class=\"p\">,<\/span> <span class=\"n\">ps<\/span><span class=\"p\">)<\/span>\n    <span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">MMFFOptimizeMoleculeConfs<\/span><span class=\"p\">(<\/span><span class=\"n\">m_h<\/span><span class=\"p\">,<\/span> <span class=\"n\">numThreads<\/span><span class=\"o\">=<\/span><span class=\"mi\">0<\/span><span class=\"p\">)<\/span> <span class=\"c1\">#ETKDG\u6cd5\u306e\u5834\u5408\u306f\u6700\u9069\u5316\u3055\u308c\u3066\u3044\u308b<\/span>\n    <span class=\"n\">prop<\/span> <span class=\"o\">=<\/span> <span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">MMFFGetMoleculeProperties<\/span><span class=\"p\">(<\/span><span class=\"n\">m_h<\/span><span class=\"p\">)<\/span>\n    <span class=\"n\">energies<\/span> <span class=\"o\">=<\/span> <span class=\"p\">[]<\/span>\n    <span class=\"k\">for<\/span> <span class=\"n\">cid<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">ids<\/span><span class=\"p\">:<\/span>\n        <span class=\"n\">ff<\/span> <span class=\"o\">=<\/span> <span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">MMFFGetMoleculeForceField<\/span><span class=\"p\">(<\/span><span class=\"n\">m_h<\/span><span class=\"p\">,<\/span> <span class=\"n\">prop<\/span><span class=\"p\">,<\/span> <span class=\"n\">confId<\/span><span class=\"o\">=<\/span><span class=\"n\">cid<\/span><span class=\"p\">)<\/span>\n        <span class=\"n\">energy<\/span> <span class=\"o\">=<\/span> <span class=\"n\">ff<\/span><span class=\"o\">.<\/span><span class=\"n\">CalcEnergy<\/span><span class=\"p\">()<\/span>\n        <span class=\"n\">energies<\/span><span class=\"o\">.<\/span><span class=\"n\">append<\/span><span class=\"p\">((<\/span><span class=\"n\">energy<\/span><span class=\"p\">,<\/span> <span class=\"n\">cid<\/span><span class=\"p\">))<\/span>\n    <span class=\"k\">return<\/span> <span class=\"n\">m_h<\/span><span class=\"p\">,<\/span> <span class=\"nb\">list<\/span><span class=\"p\">(<\/span><span class=\"n\">ids<\/span><span class=\"p\">),<\/span> <span class=\"n\">energies<\/span>\n\n<span class=\"c1\"># \u5165\u529b\u3057\u305f\u5206\u5b50\u306fm, \u751f\u6210\u3057\u305f\u30b3\u30f3\u30db\u30de\u30fc\u306fconformers\u3068\u3057\u3066\u8fd4\u3059\u3002<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3092n\u500b\u767a\u751f\">\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u3092n\u500b\u767a\u751f<\/h3>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[4]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"o\">%%time<\/span>\n<span class=\"n\">m<\/span><span class=\"p\">,<\/span> <span class=\"n\">ids<\/span><span class=\"p\">,<\/span> <span class=\"n\">energies<\/span> <span class=\"o\">=<\/span> <span class=\"n\">generateconformations<\/span><span class=\"p\">(<\/span><span class=\"n\">mol<\/span><span class=\"p\">,<\/span><span class=\"n\">n<\/span><span class=\"p\">)<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"Number of generated conformers:\"<\/span><span class=\"p\">,<\/span> <span class=\"nb\">len<\/span><span class=\"p\">(<\/span><span class=\"n\">ids<\/span><span class=\"p\">))<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>Number of generated conformers: 209\nCPU times: user 3min 16s, sys: 18.7 ms, total: 3min 16s\nWall time: 6.21 s\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[5]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"c1\">#\u30b3\u30f3\u30db\u30de\u30fc\u306e\u30a2\u30e9\u30a4\u30f3\u30e1\u30f3\u30c8<\/span>\n<span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">AlignMolConformers<\/span><span class=\"p\">(<\/span><span class=\"n\">m<\/span><span class=\"p\">)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[6]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">sort<\/span> <span class=\"o\">=<\/span> <span class=\"n\">np<\/span><span class=\"o\">.<\/span><span class=\"n\">argsort<\/span><span class=\"p\">([<\/span><span class=\"n\">energy<\/span><span class=\"p\">[<\/span><span class=\"mi\">0<\/span><span class=\"p\">]<\/span> <span class=\"k\">for<\/span> <span class=\"n\">energy<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">energies<\/span><span class=\"p\">])<\/span> <span class=\"c1\">#arsort\u306f\u5024\u3067\u306f\u306a\u304f\u4e26\u3073\u66ff\u3048\u305f\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u3092\u8fd4\u3059<\/span>\n<span class=\"n\">energy_sorted<\/span> <span class=\"o\">=<\/span> <span class=\"n\">np<\/span><span class=\"o\">.<\/span><span class=\"n\">sort<\/span><span class=\"p\">([<\/span><span class=\"n\">energy<\/span><span class=\"p\">[<\/span><span class=\"mi\">0<\/span><span class=\"p\">]<\/span> <span class=\"k\">for<\/span> <span class=\"n\">energy<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">energies<\/span><span class=\"p\">])<\/span>\n\n<span class=\"c1\"># \u30a8\u30cd\u30eb\u30ae\u30fc\u9806\u306b\u30b3\u30f3\u30db\u30de\u30fc\u3092\u4e26\u3079\u66ff\u3048\u305f\u65b0\u3057\u3044\u5206\u5b50\u3092\u4f5c\u308b\u3002<\/span>\n<span class=\"n\">m_sorted<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Chem<\/span><span class=\"o\">.<\/span><span class=\"n\">Mol<\/span><span class=\"p\">(<\/span><span class=\"n\">m<\/span><span class=\"p\">)<\/span>\n<span class=\"n\">m_sorted<\/span><span class=\"o\">.<\/span><span class=\"n\">RemoveAllConformers<\/span><span class=\"p\">()<\/span>\n<span class=\"n\">conf_ids<\/span> <span class=\"o\">=<\/span> <span class=\"p\">[<\/span><span class=\"n\">conf<\/span><span class=\"o\">.<\/span><span class=\"n\">GetId<\/span><span class=\"p\">()<\/span> <span class=\"k\">for<\/span> <span class=\"n\">conf<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">m<\/span><span class=\"o\">.<\/span><span class=\"n\">GetConformers<\/span><span class=\"p\">()]<\/span>\n<span class=\"k\">for<\/span> <span class=\"n\">i<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">sort<\/span><span class=\"p\">:<\/span>\n    <span class=\"n\">conf<\/span> <span class=\"o\">=<\/span> <span class=\"n\">m<\/span><span class=\"o\">.<\/span><span class=\"n\">GetConformer<\/span><span class=\"p\">(<\/span><span class=\"n\">conf_ids<\/span><span class=\"p\">[<\/span><span class=\"n\">i<\/span><span class=\"p\">])<\/span>\n    <span class=\"n\">m_sorted<\/span><span class=\"o\">.<\/span><span class=\"n\">AddConformer<\/span><span class=\"p\">(<\/span><span class=\"n\">conf<\/span><span class=\"p\">,<\/span> <span class=\"n\">assignId<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"\u30af\u30e9\u30b9\u30bf\u30ea\u30f3\u30b0\">\u30af\u30e9\u30b9\u30bf\u30ea\u30f3\u30b0<\/h3>\n<ul>\n<li><a href=\"https:\/\/doi.org\/10.1021\/ci2002318\">Schulz-Gasch, T.; Sch\u00e4rfer, C.; Guba, W.; Rarey, M. TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. <em>J. Chem. Inf. Model<\/em>. <strong>2012<\/strong>, <em>52<\/em>, 1499-1512<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[7]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"c1\"># \u6c34\u7d20\u539f\u5b50\u3092\u524a\u9664<\/span>\n<span class=\"n\">m_noh<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Chem<\/span><span class=\"o\">.<\/span><span class=\"n\">RemoveHs<\/span><span class=\"p\">(<\/span><span class=\"n\">m_sorted<\/span><span class=\"p\">)<\/span>\n<span class=\"c1\"># RMS\u884c\u5217\uff08RMS matrix\uff09<\/span>\n<span class=\"n\">rmsmat<\/span> <span class=\"o\">=<\/span> <span class=\"n\">AllChem<\/span><span class=\"o\">.<\/span><span class=\"n\">GetConformerRMSMatrix<\/span><span class=\"p\">(<\/span><span class=\"n\">m_noh<\/span><span class=\"p\">,<\/span> <span class=\"n\">prealigned<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">)<\/span>\n<span class=\"c1\"># TFD\u884c\u5217\uff08TFD matrix\uff09<\/span>\n<span class=\"n\">tfdmat<\/span> <span class=\"o\">=<\/span> <span class=\"n\">TorsionFingerprints<\/span><span class=\"o\">.<\/span><span class=\"n\">GetTFDMatrix<\/span><span class=\"p\">(<\/span><span class=\"n\">m_noh<\/span><span class=\"p\">)<\/span>\n<span class=\"c1\"># \u30af\u30e9\u30b9\u30bf\u30ea\u30f3\u30b0<\/span>\n<span class=\"n\">num<\/span> <span class=\"o\">=<\/span> <span class=\"n\">m_noh<\/span><span class=\"o\">.<\/span><span class=\"n\">GetNumConformers<\/span><span class=\"p\">()<\/span>\n<span class=\"n\">rms_clusters<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Butina<\/span><span class=\"o\">.<\/span><span class=\"n\">ClusterData<\/span><span class=\"p\">(<\/span><span class=\"n\">rmsmat<\/span><span class=\"p\">,<\/span> <span class=\"n\">num<\/span><span class=\"p\">,<\/span> <span class=\"mf\">0.5<\/span><span class=\"p\">,<\/span> <span class=\"n\">isDistData<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">,<\/span> <span class=\"n\">reordering<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">)<\/span>\n<span class=\"n\">tfd_clusters<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Butina<\/span><span class=\"o\">.<\/span><span class=\"n\">ClusterData<\/span><span class=\"p\">(<\/span><span class=\"n\">tfdmat<\/span><span class=\"p\">,<\/span> <span class=\"n\">num<\/span><span class=\"p\">,<\/span> <span class=\"mf\">0.04<\/span><span class=\"p\">,<\/span> <span class=\"n\">isDistData<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">,<\/span> <span class=\"n\">reordering<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">)<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'Number of RMS clusters:'<\/span><span class=\"p\">,<\/span> <span class=\"nb\">len<\/span><span class=\"p\">(<\/span><span class=\"n\">rms_clusters<\/span><span class=\"p\">))<\/span>\n<span class=\"c1\">#for i in range(len(rms_clusters)):<\/span>\n<span class=\"c1\">#    print('RMS cluster_{}:'.format(i), rms_clusters[i])<\/span>\n<span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'<\/span><span class=\"se\">\\n<\/span><span class=\"s1\">Number of TFD clusters:'<\/span><span class=\"p\">,<\/span> <span class=\"nb\">len<\/span><span class=\"p\">(<\/span><span class=\"n\">tfd_clusters<\/span><span class=\"p\">))<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>Number of RMS clusters: 47\n\nNumber of TFD clusters: 7\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"SDF\u30d5\u30a1\u30a4\u30eb\u306b\u4fdd\u5b58\">SDF\u30d5\u30a1\u30a4\u30eb\u306b\u4fdd\u5b58<\/h3>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[8]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">writer<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Chem<\/span><span class=\"o\">.<\/span><span class=\"n\">SDWriter<\/span><span class=\"p\">(<\/span><span class=\"s2\">\".\/conformers.sdf\"<\/span><span class=\"p\">)<\/span>\n<span class=\"k\">for<\/span> <span class=\"n\">i<\/span> <span class=\"ow\">in<\/span> <span class=\"nb\">range<\/span><span class=\"p\">(<\/span><span class=\"n\">m_sorted<\/span><span class=\"o\">.<\/span><span class=\"n\">GetNumConformers<\/span><span class=\"p\">()):<\/span>\n    <span class=\"n\">writer<\/span><span class=\"o\">.<\/span><span class=\"n\">write<\/span><span class=\"p\">(<\/span><span class=\"n\">m_sorted<\/span><span class=\"p\">,<\/span> <span class=\"n\">confId<\/span><span class=\"o\">=<\/span><span class=\"n\">i<\/span><span class=\"p\">)<\/span>\n<span class=\"n\">writer<\/span><span class=\"o\">.<\/span><span class=\"n\">close<\/span><span class=\"p\">()<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"Pandas\u3092\u4f7f\u3063\u3066\u30c6\u30fc\u30d6\u30eb\u306b\u3059\u308b\">Pandas\u3092\u4f7f\u3063\u3066\u30c6\u30fc\u30d6\u30eb\u306b\u3059\u308b<\/h3>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[9]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">df<\/span> <span class=\"o\">=<\/span> <span class=\"n\">PandasTools<\/span><span class=\"o\">.<\/span><span class=\"n\">LoadSDF<\/span><span class=\"p\">(<\/span><span class=\"s1\">'.\/conformers.sdf'<\/span><span class=\"p\">,<\/span> <span class=\"n\">removeHs<\/span><span class=\"o\">=<\/span><span class=\"kc\">False<\/span><span class=\"p\">)<\/span> <span class=\"c1\"># \u6c34\u7d20\u539f\u5b50\u3082\u8aad\u307f\u8fbc\u3080<\/span>\n<span class=\"n\">df<\/span><span class=\"p\">[<\/span><span class=\"s1\">'MMFF_Energy'<\/span><span class=\"p\">]<\/span> <span class=\"o\">=<\/span> <span class=\"p\">[<\/span><span class=\"n\">E<\/span> <span class=\"k\">for<\/span> <span class=\"n\">E<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">energy_sorted<\/span><span class=\"p\">]<\/span> <span class=\"c1\"># Dataframe\u306b\u65b0\u305f\u306a\u5217\u3092\u8ffd\u52a0<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u306e\u53ef\u8996\u5316\">\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u306e\u53ef\u8996\u5316<\/h3>\n<p>NGLView\u3092\u4f7f\u7528\u3057\u3066\u6700\u5b89\u5b9a\u30b3\u30f3\u30db\u30de\u30fc\u3092\u8868\u793a<\/p>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[10]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"nb\">print<\/span><span class=\"p\">([<\/span><span class=\"n\">r<\/span><span class=\"p\">[<\/span><span class=\"mi\">0<\/span><span class=\"p\">]<\/span> <span class=\"k\">for<\/span> <span class=\"n\">r<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">rms_clusters<\/span><span class=\"p\">])<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div class=\"output_subarea output_stream output_stdout output_text\">\n<pre>[158, 156, 154, 109, 82, 73, 37, 192, 88, 57, 51, 160, 195, 141, 91, 56, 157, 100, 208, 203, 102, 26, 197, 186, 175, 159, 150, 131, 111, 75, 32, 3, 206, 140, 106, 74, 44, 199, 188, 187, 183, 172, 123, 76, 54, 53, 48]\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[11]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">confid<\/span> <span class=\"o\">=<\/span> <span class=\"mi\">0<\/span>\n<span class=\"n\">view<\/span> <span class=\"o\">=<\/span> <span class=\"n\">nglview<\/span><span class=\"o\">.<\/span><span class=\"n\">show_rdkit<\/span><span class=\"p\">(<\/span><span class=\"n\">df<\/span><span class=\"o\">.<\/span><span class=\"n\">loc<\/span><span class=\"p\">[<\/span><span class=\"n\">confid<\/span><span class=\"p\">,<\/span> <span class=\"s1\">'ROMol'<\/span><span class=\"p\">])<\/span> <span class=\"c1\"># MMFF\u529b\u5834\u3067\u306e\u6700\u5b89\u5b9a\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3<\/span>\n<span class=\"n\">view<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div id=\"062c9ad6-4f56-4f8f-821a-9196d06f1a0e\">&nbsp;<\/div>\n<div class=\"output_subarea output_widget_view \"><script type=\"text\/javascript\"><br \/>\nvar element = $('#062c9ad6-4f56-4f8f-821a-9196d06f1a0e');<br \/>\n<\/script><br \/>\n<script type=\"application\/vnd.jupyter.widget-view+json\"><br \/>\n{\"model_id\": \"a7ed5a65351d4c13bd90c7ab326b44aa\", \"version_major\": 2, \"version_minor\": 0}<br \/>\n<\/script><\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[12]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">view<\/span><span class=\"o\">.<\/span><span class=\"n\">render_image<\/span><span class=\"p\">()<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"output_wrapper\">\n<div class=\"output\">\n<div class=\"output_area\">\n<div class=\"prompt\">&nbsp;<\/div>\n<div id=\"69005644-5f38-4d40-90f6-004aec630ffc\">&nbsp;<\/div>\n<div class=\"output_subarea output_widget_view \"><script type=\"text\/javascript\"><br \/>\nvar element = $('#69005644-5f38-4d40-90f6-004aec630ffc');<br \/>\n<\/script><br \/>\n<script type=\"application\/vnd.jupyter.widget-view+json\"><br \/>\n{\"model_id\": \"1b22ba60079e4d188a2d9082fdc1d261\", \"version_major\": 2, \"version_minor\": 0}<br \/>\n<\/script><\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h2 id=\"QM\u8a08\u7b97\u306b\u3088\u308b\u6bd4\u8f03\">QM\u8a08\u7b97\u306b\u3088\u308b\u6bd4\u8f03<\/h2>\n<p>\u624b\u6cd5\uff1a <strong>B97-3c<\/strong>: 2018\u5e74\u306b\u767a\u8868\u3055\u308c\u305fDFT\u6cd5\u306e\u4e00\u7a2e\u3002<\/p>\n<ul>\n<li><a href=\"https:\/\/computational-chemistry.com\/top\/blog\/2018\/01\/10\/b97_functional\/\">B97<\/a>: 1997\u5e74\u306b\u767a\u8868\u3055\u308c\u305f\u6c4e\u95a2\u6570<\/li>\n<li>3c: &#8220;three-fold corrected&#8221;<\/li>\n<\/ul>\n<p>\u57fa\u5e95\u95a2\u6570\u5f62\u306fdef2-mTZVP\u304c\u4f7f\u308f\u308c\u308b\u3002<\/p>\n<ul>\n<li><a href=\"https:\/\/doi.org\/10.1063\/1.5012601\">Brandenburg, J. G.; Bannwarth, C.; Hansen, A.; Grimme, S. B97-3c: A revised low-cost variant of the B97-D density functional method. <em>J. Chem. Phys<\/em>. <strong>2018<\/strong>, <em>148<\/em>, 064104. DOI: 10.1063\/1.5012601<\/a><\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.23317\">Sure, R.; Grimme, S. Corrected small basis set Hartree\u2010Fock method for large systems. <em>J. Comput. Chem<\/em>. <strong>2013<\/strong>, <em>34<\/em>, 1672-1685. DOI: 10.1002\/jcc.23317<\/a><\/li>\n<\/ul>\n<p>Intel CPU\u306fHyper-Threading Technology\u3092\u5229\u7528\u3057\u30661\u30b3\u30a2\/2\u30b9\u30ec\u30c3\u30c9\u3067\u52d5\u4f5c\u3057\u307e\u3059\u304c\u3001mpirun\u306f &#8220;&#8211;use-hwthread-cpus&#8221; \u30aa\u30d7\u30b7\u30e7\u30f3\u3092\u4ed8\u3051\u3066\u5b9f\u884c\u3057\u306a\u3051\u308c\u3070\u3001\u7269\u7406\u7684\u306a\u30b3\u30a2\u6570\u307e\u3067\u3057\u304b\u4e26\u5217\u8a08\u7b97\u3092\u3057\u3066\u304f\u308c\u306a\u3044\u3002\u7269\u7406\u30b3\u30a2\u6570\u4ee5\u5185\u3067\u3082\u3001qsub\u304b\u3089\u30b8\u30e7\u30d6\u3092\u9001\u308b\u3068\u6b62\u307e\u308b\u3002\u30b3\u30de\u30f3\u30c9\u30e9\u30a4\u30f3\u304b\u3089\u3060\u3068\u5927\u4e08\u592b\u306a\u6642\u3082\u3042\u308b\u304c\u3001\u6b62\u307e\u308b\u6642\u306f\u6b62\u307e\u308b\u3002\u7406\u7531\u4e0d\u660e\u3002<\/p>\n<p>ORCA finished by error termination in SCF<\/p>\n<p>&#8230;. aborting the run<\/p>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[13]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"k\">def<\/span> <span class=\"nf\">GenOrcaInput<\/span><span class=\"p\">(<\/span><span class=\"n\">i<\/span><span class=\"p\">,<\/span> <span class=\"n\">method<\/span><span class=\"o\">=<\/span><span class=\"s1\">'B97-3c'<\/span><span class=\"p\">,<\/span> <span class=\"n\">thread<\/span><span class=\"o\">=<\/span><span class=\"mi\">4<\/span><span class=\"p\">):<\/span>\n    <span class=\"n\">conf<\/span> <span class=\"o\">=<\/span> <span class=\"n\">df<\/span><span class=\"o\">.<\/span><span class=\"n\">at<\/span><span class=\"p\">[<\/span><span class=\"n\">i<\/span><span class=\"p\">,<\/span> <span class=\"s1\">'ROMol'<\/span><span class=\"p\">]<\/span>\n    <span class=\"n\">molBlock<\/span> <span class=\"o\">=<\/span> <span class=\"n\">Chem<\/span><span class=\"o\">.<\/span><span class=\"n\">MolToMolBlock<\/span><span class=\"p\">(<\/span><span class=\"n\">conf<\/span><span class=\"p\">)<\/span>\n    <span class=\"c1\"># \u539f\u5b50\u6570\u3092\u53d6\u5f97<\/span>\n    <span class=\"n\">num<\/span> <span class=\"o\">=<\/span> <span class=\"n\">conf<\/span><span class=\"o\">.<\/span><span class=\"n\">GetNumAtoms<\/span><span class=\"p\">()<\/span>\n    <span class=\"c1\"># \u5168\u3066\u306e\u884c\u3092\u30ea\u30b9\u30c8\u3068\u3057\u3066\u4fdd\u5b58\u3059\u308b<\/span>\n    <span class=\"n\">lst_molBlock<\/span> <span class=\"o\">=<\/span> <span class=\"n\">molBlock<\/span><span class=\"o\">.<\/span><span class=\"n\">split<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"<\/span><span class=\"se\">\\n<\/span><span class=\"s2\">\"<\/span><span class=\"p\">)<\/span>\n    <span class=\"c1\"># 4\u884c\u76ee\u304b\u3089\uff084+\u539f\u5b50\u6570\uff09\u884c\u76ee\u307e\u3067\u306e\u5404\u884c\u3092\u629c\u304d\u51fa\u3059<\/span>\n    <span class=\"n\">coordinates_part<\/span> <span class=\"o\">=<\/span> <span class=\"n\">lst_molBlock<\/span><span class=\"p\">[<\/span><span class=\"mi\">4<\/span> <span class=\"p\">:<\/span> <span class=\"mi\">4<\/span> <span class=\"o\">+<\/span> <span class=\"n\">num<\/span><span class=\"p\">]<\/span>\n    <span class=\"c1\"># \u539f\u5b50\u306e\u7a2e\u985e\u3068\u5404\u5ea7\u6a19\u3092\u30bf\u30d7\u30eb\u3068\u3057\u3066\u4fdd\u5b58<\/span>\n    <span class=\"n\">coordinates<\/span> <span class=\"o\">=<\/span> <span class=\"p\">[(<\/span><span class=\"n\">atoms<\/span><span class=\"p\">[<\/span><span class=\"mi\">31<\/span><span class=\"p\">],<\/span><span class=\"n\">atoms<\/span><span class=\"p\">[<\/span><span class=\"mi\">0<\/span><span class=\"p\">:<\/span><span class=\"mi\">30<\/span><span class=\"p\">])<\/span> <span class=\"k\">for<\/span> <span class=\"n\">atoms<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">coordinates_part<\/span><span class=\"p\">]<\/span>\n    <span class=\"n\">os<\/span><span class=\"o\">.<\/span><span class=\"n\">makedirs<\/span><span class=\"p\">(<\/span><span class=\"s1\">'conf<\/span><span class=\"si\">{}<\/span><span class=\"s1\">'<\/span><span class=\"o\">.<\/span><span class=\"n\">format<\/span><span class=\"p\">(<\/span><span class=\"n\">i<\/span><span class=\"p\">),<\/span> <span class=\"n\">exist_ok<\/span><span class=\"o\">=<\/span><span class=\"kc\">True<\/span><span class=\"p\">)<\/span>\n    <span class=\"k\">with<\/span> <span class=\"nb\">open<\/span><span class=\"p\">(<\/span><span class=\"s1\">'conf<\/span><span class=\"si\">{}<\/span><span class=\"s1\">\/conf<\/span><span class=\"si\">{}<\/span><span class=\"s1\">_<\/span><span class=\"si\">{}<\/span><span class=\"s1\">.inp'<\/span><span class=\"o\">.<\/span><span class=\"n\">format<\/span><span class=\"p\">(<\/span><span class=\"n\">i<\/span><span class=\"p\">,<\/span> <span class=\"n\">i<\/span><span class=\"p\">,<\/span> <span class=\"n\">method<\/span><span class=\"o\">.<\/span><span class=\"n\">replace<\/span><span class=\"p\">(<\/span><span class=\"s1\">' '<\/span><span class=\"p\">,<\/span> <span class=\"s1\">'_'<\/span><span class=\"p\">)),<\/span> <span class=\"s1\">'w'<\/span><span class=\"p\">)<\/span> <span class=\"k\">as<\/span> <span class=\"n\">f<\/span><span class=\"p\">:<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'#'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'# conformer<\/span><span class=\"si\">{}<\/span><span class=\"s1\">'<\/span><span class=\"o\">.<\/span><span class=\"n\">format<\/span><span class=\"p\">(<\/span><span class=\"n\">i<\/span><span class=\"p\">),<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'#'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'! <\/span><span class=\"si\">{}<\/span><span class=\"s1\">'<\/span><span class=\"o\">.<\/span><span class=\"n\">format<\/span><span class=\"p\">(<\/span><span class=\"n\">method<\/span><span class=\"p\">),<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'! OPT FREQ'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span> <span class=\"c1\"># \u69cb\u9020\u6700\u9069\u5316\u3068\u632f\u52d5\u8a08\u7b97<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'%pal'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span> <span class=\"c1\"># \u4e26\u5217\u8a08\u7b97<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'nprocs <\/span><span class=\"si\">{}<\/span><span class=\"s1\">'<\/span><span class=\"o\">.<\/span><span class=\"n\">format<\/span><span class=\"p\">(<\/span><span class=\"n\">thread<\/span><span class=\"p\">),<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span> <span class=\"c1\"># \u30b9\u30ec\u30c3\u30c9\u6570<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'end'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'* xyz 0 1'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"k\">for<\/span> <span class=\"n\">atom<\/span><span class=\"p\">,<\/span> <span class=\"n\">xyz<\/span> <span class=\"ow\">in<\/span> <span class=\"n\">coordinates<\/span><span class=\"p\">:<\/span>\n            <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'<\/span><span class=\"si\">{}<\/span><span class=\"se\">\\t<\/span><span class=\"si\">{}<\/span><span class=\"s1\">'<\/span><span class=\"o\">.<\/span><span class=\"n\">format<\/span><span class=\"p\">(<\/span><span class=\"n\">atom<\/span><span class=\"p\">,<\/span> <span class=\"n\">xyz<\/span><span class=\"p\">),<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n        <span class=\"nb\">print<\/span><span class=\"p\">(<\/span><span class=\"s1\">'*'<\/span><span class=\"p\">,<\/span> <span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"n\">f<\/span><span class=\"p\">)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[14]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">num_calc<\/span> <span class=\"o\">=<\/span> <span class=\"mi\">4<\/span> <span class=\"c1\">#\u8a08\u7b97\u3059\u308b\u4e0a\u4f4d\u30b3\u30f3\u30db\u30de\u30fc\u6570<\/span>\n<span class=\"n\">method<\/span> <span class=\"o\">=<\/span> <span class=\"s2\">\"B97-3c\"<\/span> <span class=\"c1\"># \u6c4e\u95a2\u6570 (functional), \u57fa\u5e95\u95a2\u6570\u7cfb (basis set) <\/span>\n<span class=\"c1\">#method=\"B3LYP def2-TZVP\"<\/span>\n<span class=\"c1\">#method=\"wB97X-D3 def2-TZVP\"<\/span>\n\n<span class=\"k\">for<\/span> <span class=\"n\">i<\/span> <span class=\"ow\">in<\/span> <span class=\"nb\">range<\/span><span class=\"p\">(<\/span><span class=\"n\">num_calc<\/span><span class=\"p\">):<\/span>\n    <span class=\"n\">GenOrcaInput<\/span><span class=\"p\">(<\/span><span class=\"n\">i<\/span><span class=\"p\">,<\/span> <span class=\"n\">method<\/span><span class=\"o\">=<\/span><span class=\"n\">method<\/span><span class=\"p\">,<\/span> <span class=\"n\">thread<\/span><span class=\"o\">=<\/span><span class=\"mi\">8<\/span><span class=\"p\">)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing text_cell rendered\">\n<div class=\"prompt input_prompt\">&nbsp;<\/div>\n<div class=\"inner_cell\">\n<div class=\"text_cell_render border-box-sizing rendered_html\">\n<h3 id=\"qsub\u7528job-script\u306e\u4f5c\u6210\">qsub\u7528job script\u306e\u4f5c\u6210<\/h3>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[15]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"n\">file<\/span><span class=\"o\">=<\/span><span class=\"nb\">open<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"orca.sh\"<\/span><span class=\"p\">,<\/span><span class=\"s2\">\"w\"<\/span><span class=\"p\">)<\/span>\n<span class=\"n\">file<\/span><span class=\"o\">.<\/span><span class=\"n\">write<\/span><span class=\"p\">(<\/span><span class=\"s2\">\"\"\"#!\/bin\/bash<\/span>\n<span class=\"s2\">#PBS -l nodes=1:ppn=8<\/span>\n\n<span class=\"s2\">cd $PBS_O_WORKDIR<\/span>\n\n<span class=\"s2\">source \/opt\/orca\/mpivars.sh<\/span>\n\n<span class=\"s2\">cd $PBS_O_WORKDIR\/conf0\/<\/span>\n<span class=\"s2\">\/opt\/orca\/orca_4_2_1_linux_x86-64_openmpi314\/orca conf0_B97-3c.inp &gt; conf0_B97-3c.out<\/span>\n<span class=\"s2\">\"\"\"<\/span><span class=\"p\">)<\/span>\n<span class=\"n\">file<\/span><span class=\"o\">.<\/span><span class=\"n\">close<\/span><span class=\"p\">()<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[21]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"c1\">#out=!{\"\/opt\/orca\/orca_4_2_1_linux_x86-64_openmpi314\/orca conf0\/conf0_B97-3c.inp &gt; conf0\/conf0_B97-3c.out\"}<\/span>\n<span class=\"c1\">#out=!{\"qsub orca.sh\"}<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[22]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"c1\">#grepout = !{\"grep 'Final\\sGibbs\\sfree\\senergy' conf0\/conf0.out\"}<\/span>\n<span class=\"c1\">#print(grepout)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[23]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"c1\"># out=!{\"\/opt\/orca\/orca_4_2_1_linux_x86-64_openmpi314\/orca conf1.inp &gt; conf1.out\"}<\/span>\n<span class=\"c1\"># 15\u5206\u5f31\u304b\u304b\u3063\u305f<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cell border-box-sizing code_cell rendered\">\n<div class=\"input\">\n<div class=\"prompt input_prompt\">In&nbsp;[24]:<\/div>\n<div class=\"inner_cell\">\n<div class=\"input_area\">\n<div class=\" highlight hl-ipython3\">\n<pre><span class=\"c1\">#grepout = !{\"grep 'Final\\sGibbs\\sfree\\senergy' conf1.out\"}<\/span>\n<span class=\"c1\">#print(grepout)<\/span>\n<\/pre>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>&nbsp; RDKit\u306b\u3088\u308b\u4f4e\u5206\u5b50\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u63a2\u7d22  &#8230;<\/p>\n","protected":false},"author":1,"featured_media":2858,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"ja","_original_post":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=2231","footnotes":""},"categories":[5],"tags":[],"class_list":["post-2231","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false],"thumbnail":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download-150x150.png",150,150,true],"medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download-300x300.png",300,300,true],"medium_large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false],"large":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false],"1536x1536":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false],"2048x2048":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false],"onepress-blog-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download-300x150.png",300,150,true],"onepress-small":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false],"onepress-medium":["https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/02\/download.png",300,300,false]},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":0,"uagb_excerpt":"&nbsp; RDKit\u306b\u3088\u308b\u4f4e\u5206\u5b50\u306e\u30b3\u30f3\u30db\u30e1\u30fc\u30b7\u30e7\u30f3\u63a2\u7d22 ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/2231","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=2231"}],"version-history":[{"count":10,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/2231\/revisions"}],"predecessor-version":[{"id":5103,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/2231\/revisions\/5103"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media\/2858"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=2231"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/categories?post=2231"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/tags?post=2231"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}