{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2008/10/25/bioclipse2-scripting-1-from-smiles-to.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/5azgt-k8a94",
      "url": "https://chem-bla-ics.linkedchemistry.info/2008/10/25/bioclipse2-scripting-1-from-smiles-to.html",
      "title": "Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol",
      "content_html": "<p>After some difficulties this week with making an export of <a href=\"http://cdk.sf.net/\">CDK</a> plugins in the\n<a href=\"http://www.bioclipse.net/\">Bioclipse2</a> <em>Cheminformatics feature</em> of with the <a href=\"http://cdk.svn.sourceforge.net/viewvc/cdk/cdk-eclipse/trunk/\">cdk-eclipse</a>\nsoftware, I got the following cute Bioclipse2 script up and running:</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nx\">dimethylether</span> <span class=\"o\">=</span> <span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">fromSMILES</span><span class=\"p\">(</span> <span class=\"dl\">\"</span><span class=\"s2\">COC</span><span class=\"dl\">\"</span> <span class=\"p\">);</span>\n<span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">addExplicitHydrogens</span><span class=\"p\">(</span> <span class=\"nx\">dimethylether</span> <span class=\"p\">);</span>\n<span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">generate3dCoordinates</span><span class=\"p\">(</span> <span class=\"nx\">dimethylether</span> <span class=\"p\">);</span>\n\n<span class=\"c1\">// save as CML</span>\n<span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">saveCML</span><span class=\"p\">(</span> <span class=\"nx\">dimethylether</span><span class=\"p\">,</span> <span class=\"dl\">\"</span><span class=\"s2\">/Virtual/dimethylether.cml</span><span class=\"dl\">\"</span> <span class=\"p\">);</span>\n<span class=\"nx\">ui</span><span class=\"p\">.</span><span class=\"nf\">open</span><span class=\"p\">(</span> <span class=\"dl\">\"</span><span class=\"s2\">/Virtual/dimethylether.cml</span><span class=\"dl\">\"</span> <span class=\"p\">);</span> <span class=\"c1\">// this should open a JmolEditor</span>\n\n<span class=\"nx\">jmol</span><span class=\"p\">.</span><span class=\"nf\">minimize</span><span class=\"p\">();</span>\n</code></pre></div></div>\n\n<p>You can see four of my favorite cheminformatics tools integrated: CDK is used to convert a SMILES into connection table with add explicit\nhydrogens, and to create initial 3D coordinates (with the code from Christian Hoppe, and thanx to Stefan for fixing that code in the\nCDK 1.1.x branch!). Then, <a href=\"http://cml.sourceforge.net/\">CMLDOM</a> is used to create and save a CML document, which is then opened into a\n<a href=\"http://www.jmol.org/\">Jmol</a> editor in Bioclipse.</p>\n\n<p>A variation of this script is visible in the following screenshot:</p>\n\n<p><img src=\"/assets/images/mashupCmldomJmolCDK.png\" alt=\"\" /></p>\n\n<p>This and other Bioclipse2 scripts I will post in <a href=\"http://gist.github.com/\">Gist</a>, a sort of <a href=\"http://en.wikipedia.org/wiki/Pastebin\">pastebin</a>\nsupporting version history, and I’ll tag them with <em>bioclipse gist</em> on <a href=\"http://delicious.com/egonw/\">delicious</a>, so that you can always\nbrowse them, comment on them, or add your own gists at\n<a href=\"http://delicious.com/tag/bioclipse+gist\">http://delicious.com/tag/bioclipse+gist</a>.</p>",
      "summary": "After some difficulties this week with making an export of CDK plugins in the Bioclipse2 Cheminformatics feature of with the cdk-eclipse software, I got the following cute Bioclipse2 script up and running:",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/mashupCmldomJmolCDK.png",
      "date_published": "2008-10-25T00:00:00+00:00",
      "date_modified": "2008-10-25T00:00:00+00:00",
      "tags": ["bioclipse","cml","cdk","jmol","eclipse","github","cheminf"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}