{
  "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/2010/09/15/cdk-137-changes-authors-and-reviewers.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/10.59350/0dk0s-f3c43",
      "url": "https://chem-bla-ics.linkedchemistry.info/2010/09/15/cdk-137-changes-authors-and-reviewers.html",
      "title": "CDK 1.3.6: the changes, authors, and reviewers",
      "content_html": "<p>The list of changes is particularly long for this development release. Therefore,\nI will list the authors and reviewers first. Note that this release also includes\nthe changes of the <a href=\"http://chem-bla-ics.blogspot.com/2010/07/cdk-126-changes-and-authors.html\">1.2.6</a>\nand <a href=\"https://chem-bla-ics.linkedchemistry.info//2010/09/12/cdk-127-changes-authors-and-reviewers.html\">CDK 1.2.7 release <i class=\"fa-solid fa-recycle fa-xs\"></i></a>.</p>\n\n<p><strong>The authors</strong><br />\nI am mildly impressed by this release’s list of authors… it is certainly not\nthe usual suspects anymore, and I would like to thank all contributors very\nmuch. Interestingly, we also see the number of places where contributions increase,\nand see patches from 7 different institutes (6 if you count the current ones)!</p>\n\n<pre>87  Egon Willighagen\n42  Gilleain Torrance\n17  Syed Asad Rahman\n 9  Rajarshi Guha\n 3  Jules Kerssemakers\n 4  Mark Rijnbeek\n 2  Andreas Truszkowski\n 2  Saravanaraj\n 1  Jonathan Alversson\n</pre>\n\n<p><strong>The reviewers</strong><br />\nThe below list has also slight gained size, and I welcome <a href=\"http://gilleain.blogspot.com/\">Gilliean</a>\nand <a href=\"http://sites.google.com/site/chembioinfo/\">Syed</a> as active reviewers.</p>\n\n<pre>56  Rajarshi  Guha \n18  Egon Willighagen \n12  Syed Asad Rahman \n 4  Gilleain Torrance\n</pre>\n\n<p><strong>The changes</strong><br />\nThe changes include bug fixes (see also the <a href=\"http://chem-bla-ics.blogspot.com/2010/07/cdk-126-changes-and-authors.html\">1.2.6</a>\nand <a href=\"https://chem-bla-ics.linkedchemistry.info//2010/09/12/cdk-127-changes-authors-and-reviewers.html\">1.2.7 release notes <i class=\"fa-solid fa-recycle fa-xs\"></i></a>),\nbut also an updated SMSD engine, a rename of the <em>IAtomType</em> method <em>getHydrogenCount()</em>\ninto <em>getImplicitHydrogenCount()</em> and of <em>MDLWriter</em> into <em>MDLV2000Writer</em>,\nand the addition of the <a href=\"http://gilleain.blogspot.com/2009/06/faulons-signatures-possible.html\">signature code by Gilleain</a>,\nand many, many small fixes.</p>\n\n<ul>\n  <li>Compare values not objects (fixes #3061263) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1e4adac\">1e4adac</a></li>\n  <li>Unit test to reproduce failing atom type perception with one of the options\nto create a -1 Integer object <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=87f8bfe\">87f8bfe</a></li>\n  <li>Smiles parser setting to preserve aromaticity as provided in the Smiles String\nitself. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ae21ee2\">ae21ee2</a></li>\n  <li>Added two further unit tests: one to see if the descriptor properly ‘ignores’\nhydrogens; a second to reproduce the numbers in the original Wiener paper\nfrom 1947 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=91c58dd\">91c58dd</a></li>\n  <li>Renabled test which was (accidentally?) outcommented when switching to JUnit4\nin commit 06a1a3dd <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ac82b12\">ac82b12</a></li>\n  <li>Added a reference to the original Wiener paper <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0c5187e\">0c5187e</a></li>\n  <li>No need to declare throws for other Exception’s if the superclass is already\ndeclared thrown itself (also, no need to define java.lang explicitly) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e73a291\">e73a291</a></li>\n  <li>Minor cleanup: corrected copyright statement; simplified JavaDoc by removing\nempty parameter table <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6292875\">6292875</a></li>\n  <li>Replaced inline citation by reference to the main bibliography <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=8ddbb1b\">8ddbb1b</a></li>\n  <li>Implementation of a descriptor to measure molecular complexity in terms of\nsp3 to sp2 ratio of carbon atoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6a6db0b\">6a6db0b</a></li>\n  <li>Updated javadocs and added extra unit test <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ac211ce\">ac211ce</a></li>\n  <li>Implementation of a descriptor to measure molecular complexity in terms of\nsp3 to sp2 ratio of carbon atoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=bd9fb4f\">bd9fb4f</a></li>\n  <li>Removed output to STDOUT <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=18f7d52\">18f7d52</a></li>\n  <li>Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=526362e\">526362e</a></li>\n  <li>Unit test for bug #3040273. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3bf8397\">3bf8397</a></li>\n  <li>Fixed hybridization information: these are sp3 hybridized systems <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e8cec0f\">e8cec0f</a></li>\n  <li>More missing elements for SMILES parsing problems reported in bug #3048501\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=bcb8432\">bcb8432</a></li>\n  <li>Unit tests for SMILES parsing bugs reported in #3048501 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=bb5ffe1\">bb5ffe1</a></li>\n  <li>Upper case the first character to also properly recognize lower cased ‘aromatic’\ntwo-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3f6056b\">3f6056b</a></li>\n  <li>JavaDoc fixes: correct @cdk.cite use, and small typo <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d097acf\">d097acf</a></li>\n  <li>Updated the JavaDoc for an API changed a while ago: the getInChIToStructure()\nmethod now takes an IChemObjectBuilder as second argument (fixes #3035890)\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3e1aba0\">3e1aba0</a></li>\n  <li>Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2a5bb6b\">2a5bb6b</a></li>\n  <li>Added the maven build file (closes #3042475) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6209a48\">6209a48</a></li>\n  <li>a)removed blank/unused methods and fixed imports Signed-off-by: Syed Asad\nRahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=911af3f\">911af3f</a></li>\n  <li>a)IMatch to Match and constructor call for state used TargetProperties for\nfaster processing Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=4a2f9c1\">4a2f9c1</a></li>\n  <li>a)Assert cleaned and fixed b)Correct ASSERT imports used <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a420b61\">a420b61</a></li>\n  <li>Removed unused code <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cb4048e\">cb4048e</a></li>\n  <li>Updated checking of indices which now are -1 if unset, instead of null <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cd8ccee\">cd8ccee</a></li>\n  <li>a) Default constructor supported as per changes in the CDK b) VFMCS index\nerror should point to -1 not null Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9c6c830\">9c6c830</a></li>\n  <li>a)Refactored matchers, atom matcher and bond matcher b)getTanimoto score fixed\nfor single atoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1dae4f2\">1dae4f2</a></li>\n  <li>Updates for the getImplicitHydrogenCount() renaming <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0f64e4d\">0f64e4d</a></li>\n  <li>The smsd module now depends on the signature module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7d5fc9d\">7d5fc9d</a></li>\n  <li>Latest SMSD code 1.2.0: Major changes are: <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7217e82\">7217e82</a></li>\n  <li>Use the factory to not depend on an implementation <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e2c8329\">e2c8329</a></li>\n  <li>Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per report #3020065\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=8ec9ad4\">8ec9ad4</a></li>\n  <li>Introduced a helper class with info about the CDK library: the version number,\nwhich is read from the build.props which is now included in the cdk-core.jar\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=5a2bc65\">5a2bc65</a></li>\n  <li>Also take into account super classes <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0de5777\">0de5777</a></li>\n  <li>Renamed MDLWriter into MDLV2000Writer (implements #3029447) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f0256d0\">f0256d0</a></li>\n  <li>Assert pattern has the expected value as first argument <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d4045cc\">d4045cc</a></li>\n  <li>Use the builder pattern to instantiate an IIsotope <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6760330\">6760330</a></li>\n  <li>MDLV2000 reader interprets D and T without M ISO line mandatory <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f6fd82b\">f6fd82b</a></li>\n  <li>Use the PT class to see if something can be an element and removing the redundant\nelement symbol info <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=937c4c7\">937c4c7</a></li>\n  <li>Fixed annotation with TestMethod, not TestClass (fixes #3016632) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9eb04e5\">9eb04e5</a></li>\n  <li>Skip inner classes for @cdk.module and @cdk.githash JavaDoc tests (fixes #3043084)\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d070396\">d070396</a></li>\n  <li>Throw a CDKException when a QUADRUPLE bond order is in the input, which is\nnot supported by the MDL/Symyx molfile format (fixes #3029352) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=32cdc48\">32cdc48</a></li>\n  <li>Deal with a special situation: pyridine N-oxide in the non-charge-separated\nrepresentation, with a N.sp2.3 nitrogen, with two double bonds. Previously,\nany ring-outward double bond would disqualify the ring as aromatic. This compound\nis now an exception. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c66039d\">c66039d</a></li>\n  <li>Assert the compound is aromatic (fixes false negative) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d1da527\">d1da527</a></li>\n  <li>Exporting the signatures jar <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7959947\">7959947</a></li>\n  <li>Removed the OpenJavaDocCheck Jazzy extension which was not supposed to go\nin; it’s not ready for prime time <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9364179\">9364179</a></li>\n  <li>Added missing dependencies (fixes failing unit tests) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e582852\">e582852</a></li>\n  <li>Added missing dependencies (fixes failing unit tests) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ef14ef0\">ef14ef0</a></li>\n  <li>Added missing dependency <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a0f22f6\">a0f22f6</a></li>\n  <li>Copy the 2D templates into the source distribution <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=5bcd111\">5bcd111</a></li>\n  <li>Added finally blocks to MolHandler to close its input streams, with proper\nlogging calls if it fails Fixes bug #3032568 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1201e01\">1201e01</a></li>\n  <li>UIT timeout fix <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=5a329d4\">5a329d4</a></li>\n  <li>Cleaned up exception handling in TemplateHandler.loadTemplates() to be more\nspecific and less pessimistic. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e1df763\">e1df763</a></li>\n  <li>QSAR descriptor values made serializeable <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2ef459c\">2ef459c</a></li>\n  <li>Fixed assertion to compare two Vector3d’s <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c133da5\">c133da5</a></li>\n  <li>Added test to assert that two Vector3d’s are identical <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6651956\">6651956</a></li>\n  <li>All methods now tested <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=004770a\">004770a</a></li>\n  <li>Hooking up test machinery <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=32155b0\">32155b0</a></li>\n  <li>Altered the getTetrahedralDescription to be get stereo and return ITetrahedralChirality.Stereo\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f61266c\">f61266c</a></li>\n  <li>Moved Stereotool to stereo package <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a99c918\">a99c918</a></li>\n  <li>Convenience method that returns chirality descriptor (R/S) given four atoms\nin priority order <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7abbdcc\">7abbdcc</a></li>\n  <li>Missing docs <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9a55100\">9a55100</a></li>\n  <li>Copyright statements <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d96f596\">d96f596</a></li>\n  <li>Just to be paranoid, test +/- tetrahedra above and below the XY plane <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e32f334\">e32f334</a></li>\n  <li>Tests for square planar shapes, trig bipyr, and oct <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=8b49490\">8b49490</a></li>\n  <li>Cleanup and fixing (I think) of the trigonal bipyramidal method <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1b01c84\">1b01c84</a></li>\n  <li>Test for 3 colinear points <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=01ae3fc\">01ae3fc</a></li>\n  <li>Better docs <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=bb38d10\">bb38d10</a></li>\n  <li>Tests for tetrahedral sign, some basic defined vectors <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=897b6ee\">897b6ee</a></li>\n  <li>Test class, and name change of distanceToPlane to show that it returns signed\n(+/-) distance <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1735551\">1735551</a></li>\n  <li>Initial go at the StereoTool - functions taken from Jmol’s smiles package\nfor 3D stereo checking <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c25591f\">c25591f</a></li>\n  <li>Updated OB note and robustified unit tests <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2b96512\">2b96512</a></li>\n  <li>Added support for multi-molecule mol2 files. Updated source and added unit\ntest and test file <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=dbd6df4\">dbd6df4</a></li>\n  <li>Updated cdk-1.2.x patches for master API <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e383f4b\">e383f4b</a></li>\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=6ef1fb1\">6ef1fb1</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=ce9b1bd\">ce9b1bd</a></li>\n  <li>Additional patch to reduce atom count on setAtom(null, int) and unit tests\nfor the setAtom(IAtom, int) behavior. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6cf95db\">6cf95db</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=23d9685\">23d9685</a></li>\n  <li>Fixed Bond() constructor to create a bond with zero atoms. Also fixed setAtom(IAtom,\nint) to increase the atom count if a null entry is filled with a non-null\nIAtom. <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=916ab96\">916ab96</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=4ac7111\">4ac7111</a></li>\n  <li>Added two unit tests for aromatic N-oxides that are the basis for failures\nin SMARTS matching <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=12fb96b\">12fb96b</a></li>\n  <li>added javadoc to IChemObjectReader explaining the split between ISimple and\nIIterating ChemObjectReaders <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1574e42\">1574e42</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=c5d4cd3\">c5d4cd3</a></li>\n  <li>Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone\nan IAtomContainer with an IBond with no IAtoms <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d71c31c\">d71c31c</a></li>\n  <li>Added unit tests for SMILES with failing atom typing, from email on the cdk-devel\nmailing list June 11 2010 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=890d0f5\">890d0f5</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=bb431e3\">bb431e3</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=3133a18\">3133a18</a></li>\n  <li>Added missing dependency <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=14003dc\">14003dc</a></li>\n  <li>Fixed unit test: surely there is no atom with symbol 0… how long has this\nbeen failing?? <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c888e4f\">c888e4f</a></li>\n  <li>Updated fingerprinter javadoc <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e6fecf2\">e6fecf2</a></li>\n  <li>Added a test class to aromaticity of three compounds: the last incorrectly\nfails <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a454ab8\">a454ab8</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=3357113\">3357113</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=0bd5b42\">0bd5b42</a></li>\n  <li>Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes\na big goof up <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cd83236\">cd83236</a></li>\n  <li>Replace special chars where spaces are supposed to occur, fixing the fail\nof the unit tests every now and then <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=483c856\">483c856</a></li>\n  <li>Merge branch ‘master’ of ssh://cdk.git.sourceforge.net/gitroot/cdk/cdk <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=eb6defd\">eb6defd</a></li>\n  <li>BooleanIOSetting to let MDLWriter output bond type 4 (aromatic) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a586d6a\">a586d6a</a></li>\n  <li>Reorderd imports <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2896226\">2896226</a></li>\n  <li>Added test cases to check that the code runs when faced with covalently bonded\nmetals. Currenly on failure is due to the presence of Pt, for which we do\nnot have a valency in AtomValence <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f32e9a2\">f32e9a2</a></li>\n  <li>chemfilter improvised Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2a7ee54\">2a7ee54</a></li>\n  <li>SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=8f3c70a\">8f3c70a</a></li>\n  <li>SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3266460\">3266460</a></li>\n  <li>added ExtAtomContainerManipulator Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d4d8339\">d4d8339</a></li>\n  <li>deleted ext Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=b44c82b\">b44c82b</a></li>\n  <li>updated SMSD code Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=eccc70d\">eccc70d</a></li>\n  <li>updated SMSD code Signed-off-by: Syed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=370a926\">370a926</a></li>\n  <li>Convenience constructors for AtomSignature that take IAtoms rather than atom\nindices <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=935b5f6\">935b5f6</a></li>\n  <li>Added missing jar meta file for the Signatures library <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=805103a\">805103a</a></li>\n  <li>Updated to reflect the upstream jar name <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d33a71a\">d33a71a</a></li>\n  <li>Abstract methods not part of API are now protected, to discourage thier use\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7a92d42\">7a92d42</a></li>\n  <li>Various fixes to tests <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=592b920\">592b920</a></li>\n  <li>Added the missing assert: runCoverageTest() returns a boolean stating the\nsuccess <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=850fd1a\">850fd1a</a></li>\n  <li>cdk.cite references for two Faulon papers <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=e7ccc4e\">e7ccc4e</a></li>\n  <li>More missing javadocs - notably the class documentation for AtomSignature\nand MoleculeSignature <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=8bd664f\">8bd664f</a></li>\n  <li>Mising constructor javadoc, and inheritdoc annotation on AtomSignature <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=88ffdd6\">88ffdd6</a></li>\n  <li>Final missing test <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cf148dd\">cf148dd</a></li>\n  <li>Atom signature test methods <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=888bf60\">888bf60</a></li>\n  <li>Molecule signature tests <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=b64c4e5\">b64c4e5</a></li>\n  <li>Signature quotient graph test method <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0d0a95e\">0d0a95e</a></li>\n  <li>Missing test for Orbit::iterator <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2609f1b\">2609f1b</a></li>\n  <li>Removed unused import <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=020fb92\">020fb92</a></li>\n  <li>Molecule From Signature Builder tests <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9d2a0c0\">9d2a0c0</a></li>\n  <li>All orbit methods tested <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7c46a7c\">7c46a7c</a></li>\n  <li>Finally correct junit annotations, and sort test <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=fba5ff5\">fba5ff5</a></li>\n  <li>BeforeClass method must be static; better clone test <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7e370a2\">7e370a2</a></li>\n  <li>Fixes some problems flagged by PMD <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cd3a866\">cd3a866</a></li>\n  <li>Use junit’s BeforeClass instead of Before annotation <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=2566b87\">2566b87</a></li>\n  <li>Added missing githash tags, to add links in the JavaDoc to the source code\nrepository <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=fc0a9f9\">fc0a9f9</a></li>\n  <li>Inherit JavaDoc where methods overwrite a super method <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d4a9436\">d4a9436</a></li>\n  <li>Fixed PMD warnings: more descriptive field names; use of Integer.valueOf()\n<a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=02020d6\">02020d6</a></li>\n  <li>Added test method annotation for the clone() method <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=cabd95f\">cabd95f</a></li>\n  <li>Removed some unnecessary imports <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=19b21a3\">19b21a3</a></li>\n  <li>Test orbit cloning <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3c85ab2\">3c85ab2</a></li>\n  <li>Improved canonical label method in graph signature <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=0bca11f\">0bca11f</a></li>\n  <li>Integer invariants, and updated signatures jarfile <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=5c838b6\">5c838b6</a></li>\n  <li>Added JavaDoc HTML generation for the signature module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7617074\">7617074</a></li>\n  <li>Hooked in PMD testing for the signature module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=7384bc3\">7384bc3</a></li>\n  <li>Defined dependencies for the test module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=132badc\">132badc</a></li>\n  <li>Hooked the signature module into the CDK build system <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=4ea7d48\">4ea7d48</a></li>\n  <li>Removed the dependency on the nonotify module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=93e0a22\">93e0a22</a></li>\n  <li>Created a CDK style module test suite <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=a9a4aa8\">a9a4aa8</a></li>\n  <li>MoleculeFromSignatureBuilder tests <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=d7bb6f6\">d7bb6f6</a></li>\n  <li>Extend from CDKTestCase and use the slow running test check <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=6969629\">6969629</a></li>\n  <li>Fixed and cleaned up molecule signature tests <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=3998ed7\">3998ed7</a></li>\n  <li>Initial commit of signature package <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ff2bdeb\">ff2bdeb</a></li>\n  <li>Added OpenJavaDocCheck 0.5 - the Jazzy spell checking extension <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=57e7eea\">57e7eea</a></li>\n  <li>specify fail behavior (returns null) in javadoc <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=bfd06db\">bfd06db</a></li>\n  <li>Added PMD tests for detecting misuse of TestClass and TestMethod, e.g. TestClass\non a method. (fixes #3014808) <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=c94ebcf\">c94ebcf</a></li>\n  <li>Removed two lines added in master to the removed doccheck target <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=9d679fe\">9d679fe</a></li>\n  <li>Merge branch ‘cdk-1.2.x’ <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=055f702\">055f702</a></li>\n  <li>Improved javadoc generation using a link tag, so that references to java library\nclasses are resolved properly <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1f8bb2d\">1f8bb2d</a></li>\n  <li>Update OpenJavaDocCheck to 0.5: fixing a few false positives <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f0c7d0c\">f0c7d0c</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=1523f66\">1523f66</a></li>\n  <li>OpenJavaDocCheck errors are fixed for SMSD related modules Signed-off-by:\nSyed Asad Rahman <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ac9384a\">ac9384a</a></li>\n  <li>solved cdk-Bugs-3006773 : small JavaDoc errors in the smsd module <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=f66a779\">f66a779</a></li>\n  <li>Fix for character spacing for “APO” line in RGFile output <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=ed510bf\">ed510bf</a></li>\n  <li>Branch open for commits for the future 1.3.6 <a href=\"http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=commit;h=1ab64ff\">1ab64ff</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=e8b13b2\">e8b13b2</a></li>\n</ul>",
      "summary": "The list of changes is particularly long for this development release. Therefore, I will list the authors and reviewers first. Note that this release also includes the changes of the 1.2.6 and CDK 1.2.7 release .",
      
      "date_published": "2010-09-15T00:00:00+00:00",
      "date_modified": "2026-10-02T00:00:00+00:00",
      "tags": ["cdk","cheminf","java"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}