{
  "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/2011/01/31/extracting-3d-coordinates-from-pdb.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/my5bc-38a88",
      "url": "https://chem-bla-ics.linkedchemistry.info/2011/01/31/extracting-3d-coordinates-from-pdb.html",
      "title": "Extracting 3D coordinates from PDB files with Groovy CDK",
      "content_html": "<p><a href=\"https://www.biostars.org/\">BioStar <i class=\"fa-solid fa-recycle fa-xs\"></i></a> featured a question today about\n<a href=\"https://www.biostars.org/p/1637/\">how to extract 3D coordinates from PDB files <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.\nNow, a simple script may actually do, and <a href=\"https://www.biostars.org/p/1637/#1640\">BioJava was mentioned too <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.\nOf course, it can also be done with the <a href=\"https://cdk.github.io\">CDK <i class=\"fa-solid fa-recycle fa-xs\"></i></a>. For example\nusing this Groovy code:</p>\n\n<div class=\"language-groovy highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"kn\">import</span> <span class=\"nn\">org.openscience.cdk.interfaces.*</span><span class=\"o\">;</span>\n<span class=\"kn\">import</span> <span class=\"nn\">org.openscience.cdk.io.*</span><span class=\"o\">;</span>\n<span class=\"kn\">import</span> <span class=\"nn\">org.openscience.cdk.tools.manipulator.*</span><span class=\"o\">;</span>\n<span class=\"kn\">import</span> <span class=\"nn\">org.openscience.cdk.io.IChemObjectReader.Mode</span><span class=\"o\">;</span>\n<span class=\"kn\">import</span> <span class=\"nn\">org.openscience.cdk.*</span><span class=\"o\">;</span>\n<span class=\"kn\">import</span> <span class=\"nn\">java.io.File</span><span class=\"o\">;</span>\n<span class=\"kn\">import</span> <span class=\"nn\">java.util.zip.GZIPInputStream</span><span class=\"o\">;</span>\n\n<span class=\"n\">reader</span> <span class=\"o\">=</span> <span class=\"k\">new</span> <span class=\"n\">PDBReader</span><span class=\"o\">(</span>\n  <span class=\"k\">new</span> <span class=\"nf\">GZIPInputStream</span><span class=\"o\">(</span>\n    <span class=\"k\">new</span> <span class=\"nf\">URL</span><span class=\"o\">(</span>\n      <span class=\"s2\">\"http://www.pdb.org/pdb/files/1CRN.pdb.gz\"</span>\n    <span class=\"o\">).</span><span class=\"na\">openStream</span><span class=\"o\">()</span>\n  <span class=\"o\">)</span>\n<span class=\"o\">);</span>\n<span class=\"n\">crambin</span> <span class=\"o\">=</span> <span class=\"n\">reader</span><span class=\"o\">.</span><span class=\"na\">read</span><span class=\"o\">(</span><span class=\"k\">new</span> <span class=\"n\">ChemFile</span><span class=\"o\">());</span>\n<span class=\"k\">for</span> <span class=\"o\">(</span><span class=\"n\">container</span> <span class=\"k\">in</span>\n     <span class=\"n\">ChemFileManipulator</span><span class=\"o\">.</span><span class=\"na\">getAllAtomContainers</span><span class=\"o\">(</span>\n       <span class=\"n\">crambin</span>\n     <span class=\"o\">))</span> <span class=\"o\">{</span>\n  <span class=\"k\">for</span> <span class=\"o\">(</span><span class=\"n\">atom</span> <span class=\"k\">in</span> <span class=\"n\">container</span><span class=\"o\">.</span><span class=\"na\">atoms</span><span class=\"o\">())</span> <span class=\"o\">{</span>\n    <span class=\"n\">println</span> <span class=\"n\">atom</span><span class=\"o\">.</span><span class=\"na\">point3d</span><span class=\"o\">;</span>\n  <span class=\"o\">}</span>\n<span class=\"o\">}</span>\n</code></pre></div></div>\n\n<p>Wondering what the <a href=\"https://doi.org/10.1186/1471-2105-10-397\">Bioclipse Scripting Language <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\nversion would look like… and, it can likely be done with Jmol script too.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C., &#38; Wikberg, J. E. (2009). Bioclipse 2: A scriptable integration platform for the life sciences. <i>BMC Bioinformatics</i>, <i>10</i>(1). https://doi.org/10.1186/1471-2105-10-397 <a href=\"https://doi.org/10.1186/1471-2105-10-397\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/1471-2105-10-397\">Scholia</a></div>\n  </div>",
      "summary": "BioStar featured a question today about how to extract 3D coordinates from PDB files . Now, a simple script may actually do, and BioJava was mentioned too . Of course, it can also be done with the CDK . For example using this Groovy code:",
      
      "date_published": "2011-01-31T00:00:00+00:00",
      "date_modified": "2026-10-21T00:00:00+00:00",
      "tags": ["cdk","groovy","pdb"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1186/1471-2105-10-397", "doi": "10.1186/1471-2105-10-397"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}