{
  "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/2006/09/22/cdk-bug-squash-party-day-3-and-4.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/zwkym-aty79",
      "url": "https://chem-bla-ics.linkedchemistry.info/2006/09/22/cdk-bug-squash-party-day-3-and-4.html",
      "title": "CDK Bug Squash Party - Day 3 and 4",
      "content_html": "<p>Because I was struggling hard with <a href=\"http://sourceforge.net/mailarchive/forum.php?thread_id=30594266&amp;forum_id=2178\">default values for cdk.interfaces fields</a>,\nI did not have time to write up the <a href=\"http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=bsp200609\">Bug Squash Party</a> report for day 3 (see also\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2006/09/18/cdk-bug-squash-party-day-1.html\">day 1 <i class=\"fa-solid fa-recycle fa-xs\"></i></a> and\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2006/09/20/cdk-bug-squash-party-day-2.html\">day 2 <i class=\"fa-solid fa-recycle fa-xs\"></i></a>).\nBut here it is.</p>\n\n<h1 id=\"day-3\">Day 3</h1>\n\n<p>Kai worked hard on getting the <code class=\"language-plaintext highlighter-rouge\">cdk.interfaces</code> API cleaned up, as <a href=\"http://wiki.cubic.uni-koeln.de/cdkwiki/doku.php?id=refactoringkernelclasses\">agreed upon earlier</a>.\nChristian added a test for the <a href=\"http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/geometry/GeometryTools.html\">RMSD calculator</a>\n(see <code class=\"language-plaintext highlighter-rouge\">getAllAtomRMSD()</code>), and cleaned up his code a bit. Stefan continued his bug-squashing on JChemPaint and fixed another one or two bugs.</p>\n\n<p>Rajarshi uploaded a patch to set undefined atomic properties, like partial and formal charges and the implicit hydrogen count, to <code class=\"language-plaintext highlighter-rouge\">UNSET</code> by default.\nHowever, this broke the CDK at many places, as apparently many class methods assume the default to be zero. After discussing the issue at the CUBIC,\nit turned out that this was sort of the intended, though undocumented, behavior: use the <a href=\"http://java.sun.com/docs/books/tutorial/java/nutsandbolts/datatypes.html\">default Java values</a>.</p>\n\n<p>And I added missing <code class=\"language-plaintext highlighter-rouge\">clone()</code> methods, closing one bug on SourceForge, added files for Eclipse to know how to build the CDK with Ant (thanx\nto Nico for similar files for <a href=\"http://www.jmol.org/\">Jmol</a>), and got CDK compiled again against <a href=\"http://www.classpath.org/\">Classpath</a>.</p>\n\n<h1 id=\"day-4\">Day 4</h1>\n\n<p>Miguel uploaded his first patched for support saving <a href=\"http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/protein/data/PDBPolymer.html\">PDBPolymer</a>\ndata structures into and restoring them again from CML, addressing an <a href=\"https://sourceforge.net/tracker/index.php?func=detail&amp;aid=1085912&amp;group_id=20024&amp;atid=120024\">almost two-year-old bug</a>.\nHe created new cdk.interfaces for them, to address module dependencies, but a large set of JUnit tests are <a href=\"http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/test/result-data.html\">yet missing</a>.</p>\n\n<p>Kai continued his cdk.interfaces refactoring, working on the more involved changes. Stefan, Tobias, and me worked on a poster and three three-fold\nflyers for our CDK booth at <a href=\"http://www.inf.uni-konstanz.de/complife06/\">CompLife2006</a>, so have not been very productive in bug squashing.\nBut we are happy with the result. Below is a screenshot on one side of the main CDK folder:</p>\n\n<p><img src=\"/assets/images/flyerScreeny.png\" alt=\"\" /></p>\n\n<p>With <a href=\"http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/junitsummary.html\">77 failing JUnit test</a>, and still a too large number of\n<a href=\"http://sourceforge.net/tracker/?atid=120024&amp;group_id=20024&amp;func=browse\">open bugs on SourceForge</a>, there is plenty of things to do today.</p>",
      "summary": "Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2 ). But here it is.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/flyerScreeny.png",
      "date_published": "2006-09-22T00:00:00+00:00",
      "date_modified": "2025-02-15T00:00:00+00:00",
      "tags": ["cdk","bsp","java","pdb","conference"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}