{
  "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/2008/02/27/cdk-is-now-available-from-your-nearest.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/g5s78-zqk90",
      "url": "https://chem-bla-ics.linkedchemistry.info/2008/02/27/cdk-is-now-available-from-your-nearest.html",
      "title": "CDK is now available from your nearest Debian mirror",
      "content_html": "<p><a href=\"https://chem-bla-ics.linkedchemistry.info/2008/02/20/cdk-close-to-entering-debian.html\">Some days have passed <i class=\"fa-solid fa-recycle fa-xs\"></i></a>,\nand the Debian mirrors have\nnow picked up the <a href=\"http://cdk.sf.net/\">CDK</a> package (unstable only so far), allowing you to <code class=\"language-plaintext highlighter-rouge\">sudo aptitude install libcdk-java</code> from\nyour favorite local mirror. The details are available from this <a href=\"http://packages.debian.org/libcdk-java\">packages.debian.org/libcdk-java</a>\npage. The fact that it is listed as contrib is a small mistake; the package is really <em>main</em> material.</p>\n\n<p>Now, also make sure to install BeanShell (<code class=\"language-plaintext highlighter-rouge\">sudo aptitude install bsh</code>), which allows you to start scripting the CDK. For example,\nconsider this simple script:</p>\n\n<div class=\"language-java highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"kn\">import</span> <span class=\"nn\">org.openscience.cdk.Atom</span><span class=\"o\">;</span>\n<span class=\"nc\">Atom</span> <span class=\"n\">atom</span> <span class=\"o\">=</span> <span class=\"k\">new</span> <span class=\"nc\">Atom</span><span class=\"o\">(</span><span class=\"s\">\"C\"</span><span class=\"o\">);</span>\n<span class=\"n\">print</span><span class=\"o\">(</span><span class=\"n\">atom</span><span class=\"o\">);</span>\n</code></pre></div></div>\n\n<p>Save this as content of a file <code class=\"language-plaintext highlighter-rouge\">simpleExample.bsh</code>, and run the bsh program to run the script. You will have to set the\n<code class=\"language-plaintext highlighter-rouge\">CLASSPATH</code>, so the full command looks like this on my Linux desktop:</p>\n\n<div class=\"language-shell highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nv\">CLASSPATH</span><span class=\"o\">=</span>/usr/share/java/cdk-interfaces.jar:/usr/share/java/cdk-core.jar:/usr/share/java/cdk-data.jar:/usr/share/java/vecmath1.2-1.14.jar bsh simpleExample.bsh\n</code></pre></div></div>\n\n<p>A wrapper script <code class=\"language-plaintext highlighter-rouge\">cdkbsh</code> that adds the CLASSPATH seems desirable here :) But you get the point.</p>\n\n<p>Interestingly, BeanShell also comes with a graphical user interface, as well as a command line based scripting environment.\nBoth make perfect set ups for quickly testing some code. The GUI version <code class=\"language-plaintext highlighter-rouge\">xbsh</code> looks like (don’t forget to set the CLASSPATH):</p>\n\n<p><img src=\"/assets/images/cdkbsh.png\" alt=\"\" /></p>",
      "summary": "Some days have passed , and the Debian mirrors have now picked up the CDK package (unstable only so far), allowing you to sudo aptitude install libcdk-java from your favorite local mirror. The details are available from this packages.debian.org/libcdk-java page. The fact that it is listed as contrib is a small mistake; the package is really main material.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/cdkbsh.png",
      "date_published": "2008-02-27T00:00:00+00:00",
      "date_modified": "2025-08-17T00:00:00+00:00",
      "tags": ["cdk","debian"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}