{
  "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/2008/12/05/cheminformatics-benchmark-project-1.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/wngzb-y3329",
      "url": "https://chem-bla-ics.linkedchemistry.info/2008/12/05/cheminformatics-benchmark-project-1.html",
      "title": "Cheminformatics Benchmark Project #1",
      "content_html": "<p>Yesterday’s blog about <a href=\"https://chem-bla-ics.linkedchemistry.info/2008/12/04/who-says-java-is-not-fast.html\">Who says Java is not fast?!? <i class=\"fa-solid fa-recycle fa-xs\"></i></a>\ncaused quite some feedback (thanx to all commenters!) with several good points. Of course, a table like that in the cinfony paper\n(see also the comments in the blogs by <a href=\"http://baoilleach.blogspot.com/2008/12/cinfony-paper-published-in-chemistry.html\">Noel</a>\n(the author) and <a href=\"https://doi.org/10.59350/1ph8m-fj607\">Rich <i class=\"fa-solid fa-recycle fa-xs\"></i></a>). Many things determine why the CDK\nmight be fastest in that table for SDF iterating. Suggestions have been that OpenBabel and RDKit may be doing much more than simple reading; Java might actually take advantage of the second core for caching file content.</p>\n\n<p><a href=\"http://www.simbiosys.ca/blog/\">ZZ</a> observed something I overlooked: calculating the molecular mass in CDK is by far slowest\nof all three toolkit, though people have suggestions on why that may is.</p>\n\n<h2 id=\"benchmarking\">Benchmarking</h2>\n\n<p>The correct way to compare toolkits, open source, proprietary, free, commercial, is to have a proper benchmark toolkit for\ncheminformatics. That’s what I am suggesting here: <a href=\"http://github.com/egonw/cheminfbenchmark/tree/master\">a project to define simple and fair benchmarks</a>.\nIt’s an open project, and anyone can contribute in order to keep tests balanced in impartial towards any tested toolkit.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Apodaca, R. (2008). Choose Java for Speed. In <i>Front Matter</i>. Front Matter. https://doi.org/10.59350/1ph8m-fj607 <a href=\"https://doi.org/10.59350/1ph8m-fj607\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.59350/1ph8m-fj607\">Scholia</a></div>\n  </div>",
      "summary": "Yesterday’s blog about Who says Java is not fast?!? caused quite some feedback (thanx to all commenters!) with several good points. Of course, a table like that in the cinfony paper (see also the comments in the blogs by Noel (the author) and Rich ). Many things determine why the CDK might be fastest in that table for SDF iterating. Suggestions have been that OpenBabel and RDKit may be doing much more than simple reading; Java might actually take advantage of the second core for caching file content.",
      
      "date_published": "2008-12-05T00:00:00+00:00",
      "date_modified": "2025-12-19T00:00:00+00:00",
      "tags": ["cheminf","cdk"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.59350/1ph8m-fj607", "doi": "10.59350/1ph8m-fj607"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}