{
  "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/2010/07/28/cdk-126-changes-and-authors.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/10.59350/89dx1-stx14",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/07/28/cdk-126-changes-and-authors.html",
      "title": "CDK 1.2.6: the changes and the authors",
      "content_html": "<p>Like all release in the 1.2 series after <a href=\"http://cdk.sf.net/\">CDK</a> 1.2.0, release <a href=\"https://sourceforge.net/projects/cdk/files/cdk/1.2.6/\">1.2.6</a>\nis a bug fix release. Anyone running a CDK 1.2 version is advised to upgrade. New in this release is the availability of a\n<a href=\"http://www.biotorrents.net/details.php?id=95\">torrent for the cdk-1.2.6.jar</a> (see\n<a href=\"https://chem-bla-ics.linkedchemistry.info/2010/04/18/bittorrents-for-science.html\">BitTorrents for Science <i class=\"fa-solid fa-recycle fa-xs\"></i></a>).\nPlease find below the changes and the authors that contributed to this release.</p>\n\n<h3 id=\"the-changes\">The changes</h3>\n\n<ul>\n<li>Updated the DebugBond unit test too now: new DebugBond() has zero atoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6ef1fb1b36\">6ef1fb1b36</a></li>\n<li>Backport patch, to make the patches compile with cdk-1.2.x <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ce9b1bd9b3\">ce9b1bd9b3</a></li>\n<li>Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6cf95db428\">6cf95db428</a></li>\n<li>Also fix the new NNBond() == 0 atoms for the nonotify module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=23d96855fa\">23d96855fa</a></li>\n<li>Fixed Bond() constructor to create a bond with zero atoms. Also fixed setAtom(IAtom, int) to increase the atom count if a null entry is filled with a non-null IAtom. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=916ab96c4e\">916ab96c4e</a></li>\n<li>Updated test to assume new Bond() creates a bond with zero atoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=4ac711194a\">4ac711194a</a></li>\n<li>Exceptions when clone atomless ISingleElectron and ILonePair too <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c5d4cd3b9e\">c5d4cd3b9e</a></li>\n<li>Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d71c31caf8\">d71c31caf8</a></li>\n<li>Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=890d0f573c\">890d0f573c</a></li>\n<li>Added the N.oxide atom type, for structures like (CH3)N=O <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=bb431e3768\">bb431e3768</a></li>\n<li>Fixed reading of SD properties: keep the first line too <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3133a18574\">3133a18574</a></li>\n<li>Added missing dependency <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=14003dce2f\">14003dce2f</a></li>\n<li>Fixed unit test: surely there is no atom with symbol 0... how long has this been failing?? <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c888e4fd44\">c888e4fd44</a></li>\n<li>Added a test class to aromaticity of three compounds: the last incorrectly fails <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a454ab84a7\">a454ab84a7</a></li>\n<li>Also except N.amide as part of an aromatic ring <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3357113d0a\">3357113d0a</a></li>\n<li>Added a test class to repeat atom type perception and test consistency <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0bd5b421d3\">0bd5b421d3</a></li>\n<li>Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cd83236c3a\">cd83236c3a</a></li>\n<li>Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=483c856e3a\">483c856e3a</a></li>\n<li>Improved javadoc generation using a link tag, so that references to java library classes are resolved properly <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1f8bb2d7a1\">1f8bb2d7a1</a></li>\n<li>Removed use of the proprietary DocCheck utility <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1523f66152\">1523f66152</a></li>\n<li>Use the new tests in more situations <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e8b13b27e2\">e8b13b27e2</a></li>\n<li>Introducing PMD test for CDK specific issues: <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=406930b292\">406930b292</a></li>\n<li>Added copyright and license header <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d6b6c65f5a\">d6b6c65f5a</a></li>\n<li>Replaced outdated URL with entry in WikiPedia (fixes #3002741) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ad2bd3ed63\">ad2bd3ed63</a></li>\n<li>Fixed a ClassCastException in a unit test; I messed up (mea culpa) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=b5fa3dca01\">b5fa3dca01</a></li>\n<li>Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=5f34897eb8\">5f34897eb8</a></li>\n<li>Added missing cloning of single electrons <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2d4c1220c3\">2d4c1220c3</a></li>\n<li>Do not try to clone the atom if it does not exist <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9672df0df7\">9672df0df7</a></li>\n<li>converted uses of indexOf to startsWith/contains <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7b9d84e44a\">7b9d84e44a</a></li>\n<li>Updated HIN reader to fix bug 2984581 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f95c6324a8\">f95c6324a8</a></li>\n<li>Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=38d5f8d191\">38d5f8d191</a></li>\n<li>Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3c1b07e26f\">3c1b07e26f</a></li>\n<li>Removed duplication of cloning. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=216c1600b9\">216c1600b9</a></li>\n<li>Apparently the super.clone() does not clone the pointer to the IAtomContainer[], causing a clone() followed by changing containers in the clone to overwrite the original IAtomContainer[]. Fixed by creating a new array. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=4e5d6a120f\">4e5d6a120f</a></li>\n<li>Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=068fb3b9b2\">068fb3b9b2</a></li>\n<li>Two more tests for the issue: atom typing works fine; aromaticity detection fails: one ring is detected as aromatic (that with two nitrogesn), so that it does not consider the double ring, marking the other ring as non-aromatic <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3be2367b36\">3be2367b36</a></li>\n<li>Fixed taking into account larger ring systems when one ring is in itself already aromatic (fixes #2976054) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=891049f59a\">891049f59a</a></li>\n<li>Fixed cloning of properties with null values by always using HashMap (fixes #2975800) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2f722f09f8\">2f722f09f8</a></li>\n<li>Added four and six coordinate neutral platinum atom types. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=407d79323e\">407d79323e</a></li>\n<li>Shortened the SMILES to only contain the aromatic atoms, allowing a foreach loop: replaced for-loop by a foreach-loop, solving also the not testing all atoms in the testAromaticty() test. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6fcc3d08a0\">6fcc3d08a0</a></li>\n<li>Added InChI, and link to existing pyrolle test, using a different SMILES <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f088cd6a39\">f088cd6a39</a></li>\n<li>Added tests for two cases of aromatic rings <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c26ae95649\">c26ae95649</a></li>\n<li>Added @cdk.bug annotation, and restricted testing to the bug <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3b08f1a5dc\">3b08f1a5dc</a></li>\n<li>Removed try/catch to retain the stacktrace of where the NPE occurs <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ce11b521e1\">ce11b521e1</a></li>\n<li>Test checking for NPE when cloning with property with null as value <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0aa632a876\">0aa632a876</a></li>\n<li>Improved JavaDoc: <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=19a976c3fa\">19a976c3fa</a></li>\n<li>Loosened the perception of N.planar3 atom types: the Hueckel system consist of more than one ring, so looking just at the ring to which the atom belongs does not make sense <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d651c2597a\">d651c2597a</a></li>\n<li>Added unit tests for atom type perception of more N.planar3 atom types <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=83423a7a30\">83423a7a30</a></li>\n<li>Removed unused import <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e1c03fbff0\">e1c03fbff0</a></li>\n<li>Removed last bits of implementation details from the API: now uses List&lt;&gt; instead of ArrayList&lt;&gt; <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7727b72d7f\">7727b72d7f</a></li>\n<li>Removed output to STDOUT <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=14e1d12d71\">14e1d12d71</a></li>\n<li>Fixed some spelling errors and added JavaDoc links <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=677b3f6336\">677b3f6336</a></li>\n<li>Synchronized behavior with the MDLV2000Reader (addressing bug #2942196) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2ceef95e74\">2ceef95e74</a></li>\n<li>Ant has a release 1.8 that should be accepted in build.xml <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=4398cc45a4\">4398cc45a4</a></li>\n<li>The IMapping interface had a class comment which probably was a copy&amp;paste artefact. Changed this. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=05c857cc4e\">05c857cc4e</a></li>\n<li>Fixed license info .meta file for JavaCC <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d9e15bbca9\">d9e15bbca9</a></li>\n<li>Bumped version to differ form the 1.2.5 release <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=17a6f08a07\">17a6f08a07</a></li>\n</ul>\n\n<h3 id=\"the-authors\">The authors</h3>\n\n<p>The below numbers are based on the number of commits, but keep in mind that some developers, like myself, need more commits for the same number of changed lines.</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>49  Egon Willighagen\n 3  Rajarshi Guha\n 2  Stefan Kuhn\n 1  Arvid Berg\n 1  Mark Rynbeek\n 1  maclean\n</code></pre></div></div>\n\n<h3 id=\"the-reviewers\">The reviewers</h3>\n\n<p>The below list is based on who signed off the patches. Anyone who reviews patches in the patch tracker can basically do this. Ask on cdk-devel on how to do this.</p>\n\n<div class=\"language-plaintext highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code>41  Rajarshi Guha\n 3  Egon Willighagen\n</code></pre></div></div>",
      "summary": "Like all release in the 1.2 series after CDK 1.2.0, release 1.2.6 is a bug fix release. Anyone running a CDK 1.2 version is advised to upgrade. New in this release is the availability of a torrent for the cdk-1.2.6.jar (see BitTorrents for Science ). Please find below the changes and the authors that contributed to this release.",
      
      "date_published": "2010-07-28T00:00:00+00:00",
      "date_modified": "2026-09-27T00:00:00+00:00",
      "tags": ["cdk"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}