New in version 1.2.3

May 25th, 2009
  • The formal charge of the IAtomcontainer is transfered to IMolecularFormula
  • Fixed bug 2787332 The old bond array in the gasteiger charge calculation was set to
  • Updated to fix bug 2788357 SMARTSQueryTool now catches TokenMgrError in the construc
  • Added new taglet to process cdk.githash tag and link Javadocs to sources in Git repo
  • Updated cdk.svnrev tags to cdk.githash tags
  • Bug_2787332. Added test for the Triclosan molecule (InChI=1S/C12H7Cl3O2/c13-7-1-3-11
  • Removed obsolete renderer code: either use cdk-1.0.x or jchempaint-primary
  • Added test for bug 2786624 in the parser test suite
  • Added links to PMD pages
  • Added link to JUnit stats
  • Added list of classes in the module, with links to Nightly@Pele
  • Added set up for creating module HTML pages
  • Added set up for creating module HTML pages

New in version 1.2.2 (May 5th, 2009)

  • Fixed links. Suboptimal, as the path is still hardcoded to a single Nightly instance, but we do not have the XML framework yet to summarize things over all Nightlies (running
  • Updated version number
  • Added test to ensure IAtomContainers are not sneaked in via IMoleculeSet.add(IAtomContainerSet)
  • Overwritten addAtomContainer(IAtomContainer, double) too, to throw an IllegalArgumentException when a non-IMolecule is passed
  • Now throws an IllegalArgumentException when it is tried to store an IAtomContainer which is not an IMolecule
  • Added unit test for #2784182
  • new test with reserpine
  • Added taglets for threading safety
  • With one atom or less, we define it to be connected, as there is no partitioning needed (fixes #2784209, NullPointerException on IAtomContainer with no atoms)
  • Added unit test for bug #2784209 which currently fails
  • More removal of explicit org.openscience.cdk package names: throws clauses
  • More removal of explicit org.openscience.cdk package names
  • More removal of explicit org.openscience.cdk package names: for new org.openscience.cdk.Foo() calls
  • Removed explicit org.openscience.cdk.interfaces packages names (fixes #2783549)
  • Removed explicit package names, in favor of imports, for org.openscience.cdk in the datadebug module (fixes #2783549)
  • Removed explicit package names, in favor of imports, for org.openscience.cdk in the data module (fixes #2783549)
  • breakout of recursion option on AllRingsFinder
  • Extraction from the string elemental formula the charge.
  • Extraction from the string elemental formula the charge.
  • Controller of the mass when it is out of the range
  • Updated to intelligently add H's to a PLANAR3 N, fixes bug 2781199
  • Added test case for bug 2781199
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace
  • calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace
  • Added a unit test to ensure SD fields are read for all molecules
  • split up test
  • new files
  • more tests for cml reading
  • Added unit test for #1848591: incorrect Murcko framework
  • Fixed cast, remove redundant full package name
  • Added unit test for #2692107
  • Fixed typo: missing 's'

New in version 1.2.1 (April 17th, 2009)

  • Fixed bug 2714283, which properly throws an exception when rings are not closed properly. If a ring is not closed with the appropriate ring number, InvalidSmilesException is thrown. Matches Daylight behavior
  • Fixed bug 2729120 and added unit test
  • Updated comment to fix bug 2768643.
  • Partial fix for bug 2719237. Made getBondOrderSum static, added unit test for it
  • Typo: proteinl -> protein
  • Made class public, to unbreak adding it to the build/*.javafiles
  • Partially fixed SMARTS matching for R0. Updated target molecule initialization to explicitly indicate atoms not in a ring and also updated RingMembership atom to do an explicit check when R0 is specified. Partially fixes bug 2587204
  • Fixed dubious equality test. A private method was checking Double objects via reference. Worked fine when they were null. Fails when we need to compare by value. Code is updated to take it into account. Added unit test (and made the method protected so that it can be tested)
  • Added test method annotation. Completes coverage for data module
  • Refactored ChiIndexUtils to make it package private. Cleans up public API, since it is only used by chi descriptor code. Updated all dependent classes. Moved test code (which needs to be filled in!) as well
  • Code cleanup of ChiIndexUtils. Converted to 1.5 idioms
  • Clean up of PathTools and added test method annotation, so that core is completely covered
  • Fixed the previous commit to edit the cdk.keyword line, not the cdk.module line
  • More consistent keywords used
  • Added a test to ensure that Integer objects are compared by value rather than reference
  • Added a test case to check that atom container diffs are correct when using deserialized objects
  • Fixed IntegerDifference so that it actually checks the integer value rather than references of the Integer object. Fixes the problem whereby an object serialized to disk and then deserialized does not match the original object (i.e., non empty diff string)
  • Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet
  • Use interface instead of implementation
  • Removed an unused import
  • Use IAtomContainer instead of IMolecule, as the actual matching is using IAtomContainers already (fixes #2686249)
  • Fixed a ClassCastException (fixes #2685134)
  • Added source attrib to fix building the Ubuntu .deb
  • Fixed Help build system: use doclet jars in develjar/; updated for new src folder src/main; removed very outdated use of rt.jar
  • Removed libdepends include for test-ioformats, which does not actually have libdepends
  • Updated so that if a target atom has no symbol (such as pseudo atoms) the match returns false (rather than an NPE)
  • Fixed proper handling of #n SMARTS querys
  • Added test case for bug 2686473
  • Added note on Ant 1.7.1 required
  • Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness
  • Fixed copyright notice for 2009
  • Fixed duplicate storage of layout templates, which only belong in the sdg module, not extra module too
  • Merge branch 'local1.2' of ../../git-svn/cdk

New in version 1.2.0 (March 12th, 2009)

  • Fixes a few SMARTS parsing problem, use of two-letter symbols and IPseudoAtom in the Fingerprinter, and adds 4 new atom type definitions, for iodine and sulphur.

New in version 1.1.5 (February 27th, 2009)

  • Mostly bug fixes.

New in version 1.1.4 (February 9th, 2009)

  • Mostly small bugfixes.

New in version 1.1.1 (November 24th, 2008)

  • Mostly small bug fixes and general code clean up.

New in version 1.1.0 (October 6th, 2008)

  • Many, many changes.