{
  "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/2009/08/07/searching-pubchem-from-within-bioclipse.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/wcms5-hqy57",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/08/07/searching-pubchem-from-within-bioclipse.html",
      "title": "Searching PubChem from within Bioclipse",
      "content_html": "<p>For the application note which we are about to submit, I was working on improving the <a href=\"http://pubchem.ncbi.nlm.nih.gov/\">PubChem</a>\n<a href=\"http://www.bioclipse.net/\">Bioclipse</a> API a bit, resulting in new <code class=\"language-plaintext highlighter-rouge\">download</code> methods:</p>\n\n<script src=\"https://gist.github.com/163281.js\"></script>\n\n<p>The search allows using <a href=\"http://pubchem.ncbi.nlm.nih.gov/help.html#PubChem_index\">PubChem Filters</a> which provides\nmany simple means to restrict the search results. For example, we can search molecules and restrict on the molecular\nweight:</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nx\">lists</span> <span class=\"o\">=</span> <span class=\"nx\">pubchem</span><span class=\"p\">.</span><span class=\"nf\">download</span><span class=\"p\">(</span><span class=\"nx\">pubchem</span><span class=\"p\">.</span><span class=\"nf\">search</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">malaria 300:500[MW]</span><span class=\"dl\">\"</span><span class=\"p\">))</span>\n</code></pre></div></div>\n\n<p>Other filters you can use in pubchem.search (provided by PubChem itself), includes (with examples):</p>\n\n<ul>\n  <li><strong>[el]</strong>: <code class=\"language-plaintext highlighter-rouge\">pubchem.search(\"Au[el]\")</code></li>\n  <li><strong>[inchi]</strong>: <code class=\"language-plaintext highlighter-rouge\">pubchem.search(\"\\\"InChI=1S/CH4/h1H4\\\"[inchi]\")</code></li>\n  <li><strong>[inchikey]</strong>: <code class=\"language-plaintext highlighter-rouge\">pubchem.search(\"VNWKTOKETHGBQD-UHFFFAOYSA-N[inchikey]\")</code></li>\n  <li><strong>[mimass]</strong>: <code class=\"language-plaintext highlighter-rouge\">pubchem.search(\"375.9785:375.9786[mimass]\")</code></li>\n</ul>\n\n<p>And many, many more… see the linked Filters page.</p>\n\n<p>Now, you surely want to look at the hits, for which we use the molecular table editor:</p>\n\n<div class=\"language-javascript highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nx\">list</span> <span class=\"o\">=</span> <span class=\"nx\">pubchem</span><span class=\"p\">.</span><span class=\"nf\">download</span><span class=\"p\">(</span><span class=\"nx\">pubchem</span><span class=\"p\">.</span><span class=\"nf\">search</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">375.9785:375.9786[mimass]</span><span class=\"dl\">\"</span><span class=\"p\">))</span>\n<span class=\"nx\">cdk</span><span class=\"p\">.</span><span class=\"nf\">saveSDFile</span><span class=\"p\">(</span><span class=\"dl\">\"</span><span class=\"s2\">/Virtual/hits.sdf</span><span class=\"dl\">\"</span><span class=\"p\">,</span> <span class=\"nx\">list</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/hits.sdf</span><span class=\"dl\">\"</span><span class=\"p\">)</span>\n</code></pre></div></div>\n\n<p>Resulting in:</p>\n\n<p><img src=\"/assets/images/pubchemSearchResults.png\" alt=\"\" /></p>",
      "summary": "For the application note which we are about to submit, I was working on improving the PubChem Bioclipse API a bit, resulting in new download methods:",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/pubchemSearchResults.png",
      "date_published": "2009-08-07T00:00:00+00:00",
      "date_modified": "2009-08-07T00:00:00+00:00",
      "tags": ["bioclipse","pubchem"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}