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CHANGELOG
---------
This changelog is automatically generated from the:

  git log --pretty=format:"* %s (%aN <%ae>)" --no-merges <LAST-TAG>..HEAD >> changelog.txt

1.3.0
-----------
* Removed old changelog files (Egon Willighagen <egonw@users.sourceforge.net>)
* Capability to read and write reaction properties information. Added theirs corresponding tests (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Fixed serialization of IAtom's with null formal charge to not cause NullPointerExceptions (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for serialization of null formal charges into the MDL molfile format (which currently fails) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a typo from the previous merge (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated Javadocs for SMARTS query tool to indicate unsupported features (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Cleaned up source file to remove spurious line endings (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Bumped version number (Egon Willighagen <egonw@users.sourceforge.net>)
* The formal charge of the IAtomcontainer is transfered to IMolecularFormula (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Fixed bug 2787332 The old bond array in the gasteiger charge calculation was set to the wrong size (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated to fix bug 2788357 SMARTSQueryTool now catches TokenMgrError in the constructor and throws a CDKException. Also added unit test to check for this (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added new taglet to process cdk.githash tag and link Javadocs to sources in Git repo (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated cdk.svnrev tags to cdk.githash tags (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Bug_2787332. Added test for the Triclosan molecule (InChI=1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,1 6H) the IPMolecularLearningDescriptor caluclation fails with java.lang.ArrayIndexOutOfBoundsException: 24. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Removed obsolete renderer code: either use cdk-1.0.x or jchempaint-primary (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test for bug 2786624 in the parser test suite (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added links to PMD pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added link to JUnit stats (Egon Willighagen <egonw@users.sourceforge.net>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* 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 different JDKs, OSs, etc) (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated version number (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test to ensure IAtomContainers are not sneaked in via IMoleculeSet.add(IAtomContainerSet) (Egon Willighagen <egonw@users.sourceforge.net>)
* Overwritten addAtomContainer(IAtomContainer, double) too, to throw an IllegalArgumentException when a non-IMolecule is passed (Egon Willighagen <egonw@users.sourceforge.net>)
* Now throws an IllegalArgumentException when it is tried to store an IAtomContainer which is not an IMolecule (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #2784182 (Egon Willighagen <egonw@users.sourceforge.net>)
* new test with reserpine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Added taglets for threading safety (Egon Willighagen <egonw@users.sourceforge.net>)
* 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) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug #2784209 which currently fails (Egon Willighagen <egonw@users.sourceforge.net>)
* More removal of explicit org.openscience.cdk package names: throws clauses (Egon Willighagen <egonw@users.sourceforge.net>)
* More removal of explicit org.openscience.cdk package names (Egon Willighagen <egonw@users.sourceforge.net>)
* More removal of explicit org.openscience.cdk package names: for new org.openscience.cdk.Foo() calls (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed explicit org.openscience.cdk.interfaces packages names (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the datadebug module (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the data module (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>)
* breakout of recursion option on AllRingsFinder (mark_rynbeek <markr@ebi.ac.uk>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Controller of the mass when it is out of the range (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Updated source and test to address review issues. Updated typos in Javadocs and added link to AllRingFinder. Move instatiation of SMARTS matcher to constructor. The element count array is now of length 120. Updated JUnit test to remove superflous prints and updated copyright (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Moved the pubchem fingerprinter to the fingerprinter module, since it needs SMARTS which is not a dependency of the standard module (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added more test cases comparing our FP's with those provided by Pubchem (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated Javadocs, cleaned up some tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test for benzene (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated SMARTS patterns to use H count specifications rather than explicit H matches (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Initial version of Pubchem fingerprints based on the public domain NCGC code. Includes unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated to intelligently add H's to a PLANAR3 N, fixes bug 2781199 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added test case for bug 2781199 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated unit tests to employ equals tests. Fixed Javadocs. Address comments wrt the original patch (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* removed needless white space (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Refactored to provide a query container specifically for pharmacophore queries. (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated the toString tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test methods for the new toString methods. Also added test method annotations (Rajarshi Guha <rajarshi.guha@gmail.com>)
* provided toString methods for the pcore query classes (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added a unit test to ensure SD fields are read for all molecules (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug 1579235, which checks for aromaticity in indolizine (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated code to use 1.5 idioms and remove use of Iterator (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added links to PMD pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added link to JUnit stats (Egon Willighagen <egonw@users.sourceforge.net>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated build system to take into account non public classes as well. Also updated ChiIndexUtils to be package private (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* split up test (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* new files (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* more tests for cml reading (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed cast, remove redundant full package name (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #2692107 (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed typo: missing 's' (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed cast, remove redundant full package name (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #2692107 (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed typo: missing 's' (Egon Willighagen <egonw@users.sourceforge.net>)
* Use the proper folder name, including the CDK version (Egon Willighagen <egonw@users.sourceforge.net>)
* 1.2.1 release being prepared (Egon Willighagen <egonw@users.sourceforge.net>)
* 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 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed bug 2729120 and added unit test (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated comment to fix bug 2768643. (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Partial fix for bug 2719237. Made getBondOrderSum static, added unit test for it (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Typo: proteinl -> protein (Egon Willighagen <egonw@users.sourceforge.net>)
* Made class public, to unbreak adding it to the build/*.javafiles (Egon Willighagen <egonw@users.sourceforge.net>)
* Partially fixed SMARTS matching for R0. Updated target molecule initialization to explicitly (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed dubious equality test. A private method was checking Double objects via reference. (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added test method annotation. Completes coverage for data module (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* 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 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Code cleanup of ChiIndexUtils. Converted to 1.5 idioms (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Clean up of PathTools and added test method annotation, so that core is completely covered (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed the previous commit to edit the cdk.keyword line, not the cdk.module line (Egon Willighagen <egonw@users.sourceforge.net>)
* More consistent keywords used (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test to ensure that Integer objects are compared by value rather than reference (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added a test case to check that atom container diffs are correct when using deserialized objects (Rajarshi Guha <rajarshi.guha@gmail.com>)
* 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) (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, one last time... Leander should work by now... (Egon Willighagen <egonw@users.sourceforge.net>)
* Use interface instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* Some other code cleanup (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, here too (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, here too (Egon Willighagen <egonw@users.sourceforge.net>)
* Use interface instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed an unused import (Egon Willighagen <egonw@users.sourceforge.net>)
* Use IAtomContainer instead of IMolecule, as the actual matching is using IAtomContainers already (fixes #2686249) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a ClassCastException (fixes #2685134) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added source attrib to fix building the Ubuntu .deb (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed Help build system: use doclet jars in develjar/; updated for new src folder src/main; removed very outdated use of rt.jar (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed libdepends include for test-ioformats, which does not actually have libdepends (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated so that if a target atom has no symbol (such as pseudo atoms) the match returns false (rather than an NPE) (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed proper handling of #n SMARTS querys (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test case for bug 2686473 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added note on Ant 1.7.1 required (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a missing dep (Egon Willighagen <egon.willighagen@gmail.com>)
* Correction of the solution (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* added method to calculate the Total Mass Number given a IMolecularFormula (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added copyright info (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added missing dep (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Rearranged the order of operations and provided a useful message. Added bug annotation (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated test to check that a aromatic molecle coming from two diferent sources (kekule and aromatic SMILES) gets represented internally as the same thing. Currently does not (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* removed "throws CDKException" from method StructureResonanceGenerator.setReactions(List<IReactionProcess> newReactionsList). And depending methods as StabilizationCharges.calculatePositive. It was producing some incoherences: org.openscience.cdk.charges.StabilizationCharges row 83: Unreachable catch block for CDKException. This exception is never thrown from the try statement body. (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Fixed a bunch of Javadoc errors (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added method to IAtomTypeMatcher to perceive types for all atoms in the container; allowing some removal of redundant calculations, and the addition of calculation of molecular properties, like aromaticity, as used in the Sybyl atom type matcher (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* added a convenience constructor to smilesgenerator, improved a test to test the aromaticity behaviour (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Fixed copyright notice for 2009 (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed duplicate storage of layout templates, which only belong in the sdg module, not extra module too (Egon Willighagen <egon.willighagen@gmail.com>)
* used interfaces where possible and updated to 1.5 idioms (Rajarshi Guha <rguha@localhost.localdomain>)
* Updated to use interfaces where possible and cleaned up code to use 1.5 idioms (Rajarshi Guha <rguha@localhost.localdomain>)
* Added unit test for a ONS Solubility solute, which fails to be parsed when RDF. But does not fail here. (egonw <egon.willighagen@gmail.com>)
* Export the jniinchi lib (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed a few test class instantiation problems (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed constructor: wrong file format; add getClassLoader() (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed for NewCDKTestCase -> CDKTestCase renaming (Egon Willighagen <egon.willighagen@gmail.com>)
* Added all existent reaction tests in MreactionTest (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added dictionary which reads from a reaction-process.owl the mechanism for specific type reaction. (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Invalid smiles string (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Set new methods to read new schemes of the reactions dictionary (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added testMethod value for Junit4 (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* For each data class, also test inherited methods for super classes implementing inherited superinterfaces (Egon Willighagen <egon.willighagen@gmail.com>)

1.3.1
-----------
* Bumped version for 1.3.1 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Added some extra lines, hopefully fixing the conflicts all the time (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed param name (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the makefp3d target to work with the current build system (Egon Willighagen <egonw@users.sourceforge.net>)
* Set up a branch for the 1.2.4 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H.  Also updated unit tests to take into account proper H matching. Added a unit test to further check H matching. (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added tests to match hydrogens (mark_rynbeek <markr@ebi.ac.uk>)
* Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator (Uli Köhler <ulikoehler@online.de>)
* Reworked the tests for bug 2898032. Updated Javadocs for smiles generator (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added unit test to confirm and check for bug 2898032 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed junior issue 1802586: Misuse of assertTrue for tested strings (Uli Köhler <ulikoehler@online.de>)
* Made the AtomContainerPermutors IAtomContainer implementation independent (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated UIT to handle single atom queries and added a unit test for bug 2888845. Also updated Javadocs to specifically note behavior of single atom queries (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch (Egon Willighagen <egonw@users.sourceforge.net>)
* Implemented instantiating custom loggers; example in the unit test class (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the use of the SystemOutLoggingTool as back up (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a ILoggerTool implementation for STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Dig up and updated the copyright history (Egon Willighagen <egonw@users.sourceforge.net>)
* Factored out initialization of the tool, to allow reusing the code for other logger class names (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved the log4j.jar depending LoggingTool into a separate module (Egon Willighagen <egonw@users.sourceforge.net>)
* Introduces the ILoggingTool interface and a factory so that CDK code no longer needs to depend on LoggingTool which depends on Apache's Log4j library. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generation of java source jars (Peter Odéus <peter.odeus@gmail.com>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added reading of E/Z stereochemistry from double bonds in MDL V2000 molfiles. (Egon Willighagen <egon.willighagen@gmail.com>)
* A minor fix to clean up a PDMD warning (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Overwrite unit tests, because there are no change events passed around at all for the NoNotification interface implementations (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit tests for IChemModel event propagation for the ICrystal field (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed propagation of change events to IChemModel when modifications are made in child IChemObjects (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed unit tests: the IChemModel.setFoo(null) should actually give a change event on the listener of the IChemModel, and not after unregistering of the Foo object. (Egon Willighagen <egonw@users.sourceforge.net>)
* Synchronized with the Blue Obelisk version (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test to the function of the new IO setting to force 2D coordinate output. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test to verify that if 2D and 3D coordinates are available, the 3D coordinates are outputted. (Egon Willighagen <egonw@users.sourceforge.net>)
* Changed IBond.get/setStereo() to use a IBond.Stereo enumeration instead of an int (fixes #2855850): (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed Taglets: only return HTML if the Tag is really given; the toString() method is given for all cases, not just when the tag is found (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the Mannhold LogP descriptor (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the Mannhold LogP descriptor to the ontology (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixeda bug which was causing various parts of the DescriptorEngine to fail - it was trying to instantiate a non-descriptor class which happens to reside in the descriptor package directory. This fix is a bit kludgy - ideally only descriptors should be in that directory (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixes ClassCastException when not IMolecule (Arvid Berg <goglepox@users.sourceforge.net>)
* Upgraded to PMD 2.4.5 with many bug fixes, giving more accurate error reports (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency on cdk-diff, being used in one of the unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed methods names to match those in the test class (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed test method name to match the expected patters, fixing a coverage test fail (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed duplicate code: MolecularFormulaTest now extends AbstractMolecularFormulaTest (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed test method annotation to point to the right method (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added modules that were missing from the PMD testing (Egon Willighagen <egonw@users.sourceforge.net>)
* Added modules that were missing from the doccheck testing (Egon Willighagen <egonw@users.sourceforge.net>)
* Added reference to IUPAC documentation about stereochemistry visualization. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <markr@ebi.ac.uk>)
* Added missing dependency introduced by the use of AbstractFingerprinterTest in test-standard. (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the unit test classes for all IFingerprinter implementations to use the new AbstractFingerprinter class; a few unit tests actually fail (Egon Willighagen <egonw@users.sourceforge.net>)
* Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations (Egon Willighagen <egonw@users.sourceforge.net>)
* Clean up of layout. (Jonathan Alversson <jonathan.alvarsson@gmail.com>)
* Fix the unit test to not give a 'input must support mark' exception on some platforms, by wrapping the InputStream in a BufferedInputStream. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies (Egon Willighagen <egonw@users.sourceforge.net>)
* Added ioformats to modules to test (Egon Willighagen <egonw@users.sourceforge.net>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where multiline field data is found. (Egon Willighagen <egonw@users.sourceforge.net>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where very much field data, like the ChEBI_complete.sdf (Egon Willighagen <egonw@users.sourceforge.net>)
* Factored out steps in reading the SD file data block (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version, to make it clear this is not the 1.2.3 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version, to make it clear this is not the 1.3.0 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed registering on the cdk.threadnonsage tag (closes #2796362) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed obsolete pattern from old svnrev tag (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed JavaDoc to remove traces of the old svnrev Tag (Egon Willighagen <egonw@users.sourceforge.net>)
* Synchronized exception message with implementation (fixes #2844333) (Egon Willighagen <egonw@users.sourceforge.net>)
* Made class private again, per authors request (Egon Willighagen <egonw@users.sourceforge.net>)
* Any class will do, not just public, final and abstract (Egon Willighagen <egonw@users.sourceforge.net>)
* Two further compile fixes after the merge with CDK 1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
* Made the class public, to fix a compile problem introduced by the merge with CDK 1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
* Added ant task to calculate JavaNCSS code statistics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added JavaNCSS 32.53 (LGPL 3.0) (Egon Willighagen <egonw@users.sourceforge.net>)
* The Pauling Electronegativity is copied in configure as well. I can't see why not copy everything we have. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Revert "added a test for bug 2831420": (Egon Willighagen <egonw@users.sourceforge.net>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <markr@ebi.ac.uk>)
* added a test for bug 2831420 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added a test for bug #2831420 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Made InChIGeneratorFactory a singleton. (jonalv <jonathan.alvarsson@gmail.com>)
* Layout. (jonalv <jonathan.alvarsson@gmail.com>)
* Added bug annotation (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* test case for bug #2846213 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Fixed perception of N.planar3 where N.sp2 was detected, by now taking into account the given hydrogen count. (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed perception of benzene with all single bond, but hydrogen count 1 and bonds flagged aromatic. In this case, the type is C.sp2 not C.sp3. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added assertions to unit test for values being not null (Egon Willighagen <egonw@users.sourceforge.net>)
* Added two unit tests for the same problem: carbon atom types are not correctly perceived if bond order info is SINGLE only, and hydrogen count and aromaticity flag is set. (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved class into a org.openscience.cdk package, which seems to work now. I'm puzzled why it did not before. Solved several unit test fails. (Egon Willighagen <egonw@users.sourceforge.net>)
* Unsealed the XOM jar to allow having the CustomSerializer (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed Javadocs error (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added support for 'public enum's (Egon Willighagen <egonw@users.sourceforge.net>)
* corrected bug in bondtools.isStereo(IAtomContainer container, IAtom stereoAtom). A comparision of atom symbols in a nested loop was using the counter of the outer loop twice. Note it worked before, because there is a sort of fallback to Morgan numbers. fallback to morgan (fixes #2830287) (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added a new test for bondtools (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Fixed inconsistency between accepts() and write: also support writing of IAtomContainerSet and IAtomContainer as accepts() indicates (fixes #2827745) (Egon Willighagen <egonw@users.sourceforge.net>)
* General test for testing consistency between write() and accepts(), testing that all accepted IChemObject's can also be written (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug #2826961: inconsistent atom typing for two SMILES. Unit test does not show a fail, ruling out a CDK bug (Egon Willighagen <egonw@users.sourceforge.net>)
* Remove erroneous throws statement (Egon Willighagen <egonw@users.sourceforge.net>)
* Bug found calculating the exact mass given a molecular formula when it is negative charged. (Miguel Rojas Cherto <miguelrojasch@gmail.com>)
* Fixed reading of the cdk/dict/data/elements.owl database which is now in OWL (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed issue 2458210: use assertNotNull(foo) etc instead of assertTrue(foo != null). (Uli Köhler <ulikoehler@online.de>)
* Added minimum equivalents for BondManipulator.getMaximumBondOrder() methods (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixes asserts: after removal *no* change should be recorded (Egon Willighagen <egonw@users.sourceforge.net>)
* Added IO option to disable generator of XML declaration statements in the output CML. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, and consistified code by always returning a List<?> of the same '?'. (And some 80 chars fixes in the JavaDocs.) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests to test that when a [Molecule|Reaction|Ring]Set has been removed from a ChemModel, the ChemModel should unregister as listener. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for event propagation from [Molecule|Reaction|Ring]Sets to ChemModel. (Egon Willighagen <egonw@users.sourceforge.net>)
* More testing of flags. (Egon Willighagen <egonw@users.sourceforge.net>)
* Fix for junior job id: [ 1837692 ] Test methods should throw only one Exception. (Paul Turner <paulturner@users.sourceforge.net>)
* Fixed missing imports and wrapped to 80 chars (Egon Willighagen <egonw@users.sourceforge.net>)
* Better excpetion handling in builder3d: (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)

1.3.2
-----------
* Use the new error reporting IO API
* Added a new IO API for reporting file format errors.
* A new test for canonicalLabeler. I first tried in an older checkout, where it failed, but it works in master. I think we can still put the test in, more tests are better.
* Unit test for bug #2944080
* Added the atom-atom mapping for all atom containing the reactant molecules
* Removed the bond mapping from the reaction. It will only contain atom-atom mapping functionality
* Initiating only one time the function LonePairElectronChecker
* Added getExampleReactants and getExpectedProducts method for all reaction.type test.
* The IMapping interface had a class comment which probably was a copy&paste artefact. Changed this.
* Fixed license info .meta file for JavaCC
* Removed bit which explain how to apply the LGPL to source (fixes #2926775)
* CDKHydrogenAdder should not attempt addImplicitHydrogen for pseudo atoms in an atom container
* Added unit test for adding hydrogens to IPseudoAtom, which current causes a NPE
* MDLV2000Reader throws exception for query bond types
* MDL reading and writing and stereo bond types
* Added a helper method GeometryTools.getRectangle2D() to get the space occupied by an IAtomContainer
* Reimplemented shiftContainer(IAtomContainer, Rectangle2D, Rectange2D, double) originally implemented as jchempaint-primary patch 9200bdc4d68dc8f70373a62eaec51357b680d5e6 by Stefan Kuhn: fixing the detection of overlap, and added missing unit tests
* Added IO option to allow saving aromatic SMILES
* Added missing unit testing for the SMILESWriter
* Moved Normalizer into a separate package, in reply to discussion around patch #2905749, making space for a uniform platform for structure normalization: cdk.normalize
* Attached are some more license files.
* The log4j.jar is version 1.2.15.
* More completed files attached.
* They were incomplete, as many other files still are.
* Fixed conflict in LICENSE file due to merge from cdk-1.2.x branch
* Added a QA target
* Use local PMD and JUnit reports if available
* Added option to run it on just one module
* Added info for dependencies
* Created a list, to be able to add license information
* Added missing copyright/license header
* Catch a SocketException when there is no internet
* Output where it is working on
* Removed empty lines
* Added initial license information, based on the information sent by Stefan
* [PATCH] SSSR Test
* Bucky ball test molecule
* Patch from Ulrich Bauer regarding ringsearch bauer@math.uni-goettingen.de
* Update code example in JavaDoc reflecting the current API (fixes #2914791)
* Minor fixes for the RasmolColors class.
* New classes for Rasmol color scheme
* Updated UIT matching for the single atom case so that it correctly handles queries that are plain atom containers
* Updated fingerprinter to fix bug 2819557. Updated JUnit tests to take into account new fingerprints. Also cleaned up the template extractor code and regenerated fingerprints for builder3d. Also updated the build file to properly include dependency jars for the makefp3d target
* Added a datafile entry for the standard module to store the VDW radii etc for the periodic table
* Fixed reading of SD file properties
* Added unit test for a MDL SD file with mutliple data fields
* Added unit test for data fields to allow to start with '>' (bug #2911300).
* Added testing that properties are read from test6.sdf
* Updated license info of third party libraries
* Fixed JavaDoc: added missing period at end of first sentence, removed useless @throws clause, added missing @cdk.bug tag
* Package fixing release: fixed building JavaDoc from source dist
* Added missing references file to the source dist (full and pure)
* Removed source folders of Doclets, which are not part of the release, and should not be compiled for JavaDoc generation anyway
* Removed java pkg removed by the periodic table patch from the Eclipse project classpath
* Made the unit test more informative
* Added test case for bug 2819557
* The AtomType(String) constructor is updated so that only formal charge is set to 0 as indicated in the Javadocs. All other fields are set ot UNSET. Javadocs were updated to make this explicit
* Updated canonical labeler to make use of the PeriodicTable class so that even if an input molecule was not configured we can still get a valid atomic number. This makes SMILES generation a little more robust (cf bug 2898032)
* Added OpenJavaDocCheck library (new BSD licensed) and written a custom JavaDoc checks.
* Additional constant
* added a constant for untyped atoms
* Updated to avoid use of deprecated StringBufferInputStream
* added a test for single-line inchi with several branches
* the inchi reader was written in such a way that it 1) needed a further line after the inchi=, which was not read, but needed to avoid npes 2) It could only process one branch on a level 3) it required the inchi line to start with INChI, newer versions require InChI= All this has been fixed
* Start angles should be different for different size rings
* Sorting of containers in a AtomContainerSet
* Added new test class to the module suite
* New comparators for AtomContainer
* Refactored periodic table element to be a standalone class, so independent of the data module. This is OK, since the class is really just a struct to hold PT data for a given element. As opposed to being a basis of an elemental representation. Also, this class is entirely private to this package, so it doesn't really matter what it is. Updated associated unit tests
* Some minor code clean up
* Updated to remove Symbols and all associated tests and usages. Replaced with PeriodicTable
* Moved PT related tests to their own package. Updated test suites
* Added method (and test) to get symbol from atomic number and also get element counts
* Updated module membership. Also made everything bu tmain PT class package private
* Moved PT related classes into their own package
* Added a test to MoleculeSetTest, which tests that the clone() does not change the MoleculeSEt
* Added some extra lines, hopefully fixing the conflicts all the time

1.3.3
---------
* Updated JavaDoc to explicitly state that g2 must be a substructure of g1 (Egon Willighagen <egonw@users.sourceforge.net>)
* More unit tests for the MCSS problem in bug report 2944080. (Egon Willighagen <egon.willighagen@gmail.com>)
* Simplified the code using the new 'T read(T)' API used in MDLV2000Reader as defined by the ISimpleChemObjectReader (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated for the new generics 'T read(T)' API in ISimpleChemObjectReader. (Egon Willighagen <egonw@users.sourceforge.net>)
* Introduced generics allowing the return type to be identical to the passed argument. It does require implementing classes to be updated with the new API too. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency, fixing the unit test reading a file from data/ (Egon Willighagen <egonw@users.sourceforge.net>)
* added working implementations for PartialFilledStructureMerger and CrossoverMachine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added working implementations for PartialFilledStructureMerger and CrossoverMachine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* tests for crossover machine and PartialFilledStructureMerger (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* tests for crossover machine and PartialFilledStructureMerger (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added dependency (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Fixed use of global isRef variable, to make it threading-safe (Egon Willighagen <egonw@users.sourceforge.net>)
* Added control 'isref' creating a CML with reaction and listmolecules (Miguel Rojas Cherto <miguelrojasch@gmail.com>)
* Removed unused import (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed last bits of implementation details from the API: now uses List<> instead of ArrayList<> (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed output to STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed some spelling errors and added JavaDoc links (Egon Willighagen <egonw@users.sourceforge.net>)
* Synchronized behavior with the MDLV2000Reader (addressing bug #2942196) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @cdk.bug tag and used interfaces where possible (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test case for GeometryTools.has2DCoordinatesNew where a mol file has a single atom with 0,0,0 as coordinate. This is not considered a 2d coordinate right now, but in a way it is one. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added a method to make cyclopentane to MoleculeFactory (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Added missing unit test for getClosestAtom(double, double, IAtomContainer, IAtom) (Egon Willighagen <egon.willighagen@gmail.com>)
* Improve performance: to find the closest atom, we do can simply use the squared distances. The smaller than relation is equivalent in normal and squared distance space. (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a unit test to see of the calculated bond length average includes bonds in all IAtomContainer's (Egon Willighagen <egon.willighagen@gmail.com>)
* Added second test for getClosestAtom(), now with more than two atoms (Egon Willighagen <egon.willighagen@gmail.com>)
* Added E and Z as allowed configurations (Egon Willighagen <egon.willighagen@gmail.com>)
* Added UP_OR_DOWN_INVERTED, which is the equivalent of UP_OR_DOWN but with a different stereocenter (Egon Willighagen <egon.willighagen@gmail.com>)
* Extended JavaDoc, explaining how these IBond.Stereo types define the stereocenter, and indicating for each type explicitly which atom is the stereocenter (Egon Willighagen <egon.willighagen@gmail.com>)
* Added convenience method to find the closest atom to a given point. (shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* unified the layout at cleanup and loading of molecules (Stefan Kuhn <shk3@users.sf.net>)
* Reimplemented shiftReactionVertical(IReaction, Rectangle2D, Rectange2D, double) originally implemented as jchempaint-primary patch 1cab8c3c9350ada9b1d054712189720c865e502a by Stefan Kuhn: now reuses other methods (fixing the movement of the reaction agents), and added missing unit tests (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a getBondLengthAverage(IReaction reaction) method, a rewritten version of 1cab8c3c9350ada9b1d054712189720c865e502a by Stefan Kuhn, and the matching unit test (Egon Willighagen <egon.willighagen@gmail.com>)
* Add a GeometryTools method to get atoms near another atom (Gilleain). Added unit test for the new method (Egon). (gilleain <gilleain@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Moved IAtomColorer and ICDKChangeListener from the standard module to the interfaces module (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated to include the float and binary information found in PubChem (Brian Gilman <gilmanb@gmail.com>)
* Ant has a release 1.8 that should be accepted in build.xml (Mark Rynbeek <markr@localhost.localdomain>)
* Master is open for patches... (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.4
--------
* RGroup queries (Mark Rynbeek <markr@localhost.localdomain>)
* Junit test data for RGroup queries (Mark Rynbeek <markr@localhost.localdomain>)
* R-group query changes for MDL reading/writing (Mark Rynbeek <markr@localhost.localdomain>)
* Fixed taking into account larger ring systems when one ring is in itself already aromatic (fixes #2976054) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed cloning of properties with null values by always using HashMap (fixes #2975800) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added four and six coordinate neutral platinum atom types. (Egon Willighagen <egonw@users.sourceforge.net>)
* 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. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added InChI, and link to existing pyrolle test, using a different SMILES (Egon Willighagen <egonw@users.sourceforge.net>)
* Added tests for two cases of aromatic rings (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Updated the OpenJavaDocCheck library to 0.3 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added @cdk.bug annotation, and restricted testing to the bug (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed try/catch to retain the stacktrace of where the NPE occurs (Egon Willighagen <egonw@users.sourceforge.net>)
* Test checking for NPE when cloning with property with null as value (Arvid Berg <goglepox@users.sourceforge.net>)
* Improved JavaDoc: (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed line lengths (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test to MDLRXNReaderTest which checks of different numbering for the same mapping gives the same result. x (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* The shiftContainer method did not correctly calculate how much the container needs to to shifted. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Some performance tuning for SmilesGenerator. In detail: - createSMILESWithoutCheckForMultipleMolecules public, so it can be called directly without doing partitioning - aromaticity detection optional - avoids unecessary BondTools.isStereo calls if non-chiral smiles is wished (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* made logging in the AllRingsFinder optional, this helps with performance. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* 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 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for atom type perception of more N.planar3 atom types (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing copyright statement and import (Egon Willighagen <egonw@users.sourceforge.net>)
* The MDLWriter ignored titles when writing a ChemModel (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Simplified the ILoggingTool interface by using Object... (Egon Willighagen <egonw@users.sourceforge.net>)
* Added IO option to allow saving aromatic SMILES (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit testing for the SMILESWriter (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.5
--------
* Fix for getBestAlignmentForLabelXY (Arvid Berg <goglepox@users.sourceforge.net>)
* Test for getBestAlignmentForLabelXY (Arvid Berg <goglepox@users.sourceforge.net>)
* Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality (Rajarshi Guha <rajarshi.guha@gmail.com>)
* fixed PMD errors on Use instanceof against interfaces not implementations and few more Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Introducing PMD test for CDK specific issues: (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed unstable forcefield code (Egon Willighagen <egonw@users.sourceforge.net>)
* Added copyright and license header (Rajarshi Guha <rajarshi.guha@gmail.com>)
* The createSMILES() methods now take IAtomContainer rather than IMolecule. Originally, IMolecule was the type since it was assumed that SMILES would only be generated for connected components - but the code already handles disconnected components. Since IAtomContainers are meant to support that, this change makes sense. Also a result is that we don't have to convert a IAtomContainer to IMolecule to generate SMILES (Rajarshi Guha <rajarshi.guha@gmail.com>)
* updated test cases Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* add on patches (Syed Asad Rahman <s9asad@gmail.com>)
* fixed makeAtomsMapOfBondsMap with test (Syed Asad Rahman <s9asad@gmail.com>)
* Emergency fix: IAminoAcid instead of AminoAcid (Egon Willighagen <egonw@users.sourceforge.net>)
* A few more interfaces instead of implementations (Egon Willighagen <egonw@users.sourceforge.net>)
* Replaced use of implementations by interfaces (Egon Willighagen <egonw@users.sourceforge.net>)
* Use an interface instead of an implementation as type (Egon Willighagen <egonw@users.sourceforge.net>)
* Use interfaces instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* MDL reading and writing atom value line, including test cases (M L Rijnbeek <markr@ebi.ac.uk>)
* Added another test to check that a query larger than the target does not match (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Test cases for MCS updated (Syed Asad Rahman <s9asad@gmail.com>)
* updated MCS solution count in the VF lib, depricated turbo MCS and provided methods for timeout (Syed Asad Rahman <s9asad@gmail.com>)
* updated test for single atom (Syed Asad Rahman <s9asad@gmail.com>)
* Replaced outdated URL with entry in WikiPedia (fixes #3002741) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed outdated JavaDoc I forgot to remove (fixes #3002409) (Egon Willighagen <egonw@users.sourceforge.net>)
* Included the qm module in the dist-all (fixes #3002622) (Egon Willighagen <egonw@users.sourceforge.net>)
* Cleaned up unthrown exceptions (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Removed use of SMARTS parser in the test code so that a new dependency is not required (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* removed unwated checks (Syed Asad Rahman <s9asad@gmail.com>)
* commented unused code (Syed Asad Rahman <s9asad@gmail.com>)
* test cases for the IQueryAtomContainer support in the SMSD with exceptions fixed (Syed Asad Rahman <s9asad@gmail.com>)
* test cases for the IQueryAtomContainer support in the SMSD (Syed Asad Rahman <s9asad@gmail.com>)
* IQuery* support for the SMSD, will help in SMART based searches (Syed Asad Rahman <s9asad@gmail.com>)
* Turbomode MCS search added (Syed Asad Rahman <s9asad@gmail.com>)
* Turbo mode MCS search added Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* removed unwanted test case Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* VF Sub search turbo mode (Syed Asad Rahman <s9asad@gmail.com>)
* Updated the SMSD code for turbo mode substructure search Refactored the SMSD class itself (Syed Asad Rahman <s9asad@gmail.com>)
* Added two test cases by Daniel from my blog: http://chem-bla-ics.blogspot.com/2010/05/cip-rules-2-parsing-and-from-smiles.html (Egon Willighagen <egonw@users.sourceforge.net>)
* Added two more unit tests, related to ring closing (Egon Willighagen <egonw@users.sourceforge.net>)
* SMILES @ and @@ chiralities are now fully read. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests with various chiral SMILES situations. (Egon Willighagen <egonw@users.sourceforge.net>)
* Implemented stereo chemistry for atoms with four ligands (Egon Willighagen <egonw@users.sourceforge.net>)
* Patch to generalize the stereo chemistry handling. (Egon Willighagen <egonw@users.sourceforge.net>)
* Minor fix to build.xml to ensure that SMSD code gets included in the large jar file (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added JavaDoc testing to the QA task; removed module-uptodate which checked if the module was already compiled causing the target to be skipped (Egon Willighagen <egonw@users.sourceforge.net>)
* I made sure the MDLV2000Reader considers 0,0,0 coordinates in files with a single atom as 2d and 3d coordinates. The MDLReader does not handle the 0,0,0 case explicitly, so I just added a test for 2d. It might be better to have uniforma handling, but I will file a bug report for that. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* The RXNReaders/Writers now all handle Atom-Atom-Mappings. This was only done in the MDLRXNReader till now (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Atom-Atom-Mapping is now read and written in MDL files. Note the reading until now was into ID field, which is not in line with description of ID field in ChemObject (Returns the identifier (ID) of this object). Also added tests for MDLWriter/Reader/2000Reader. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Flexibility for ring start angles. (mark_rynbeek <markr@ebi.ac.uk>)
* more mdl reader writer tests (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Revert "Additional constant" (Stefan Kuhn <stefan.kuhn@ebi.ac.uk>)
* Added a test case for short line mol files. Patch by S.Kuhn, reworked by M.Rijnbeek. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* MDL reading and writing UP_OR_DOWN (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed the R-based model package and associated jar files and test code (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed the R-based model package and associated jar files and test code (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed DocCheck from Eclipse' Build Path (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed obsolete castings, or replaced by more general ones (Egon Willighagen <egonw@users.sourceforge.net>)
* added  @Test Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* added CDKRMapHandlerTest (Syed Asad Rahman <s9asad@gmail.com>)
* added CDKRMapHandlerTest Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* The big SMSD patch. (Syed Asad Rahman <asad@ebi.ac.uk>)
* Fixed a ClassCastException in a unit test; I messed up (mea culpa) (Egon Willighagen <egonw@users.sourceforge.net>)
* Copied code from the DefaultChemObjectBuilder to handle the IBond constructor that takes an IAtom[] which I had forgotten to port to DebugChemObjectBuilder and NoNotificationChemObjectBuilder (fixes a few regressions) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing cloning of single electrons (Egon Willighagen <egonw@users.sourceforge.net>)
* Do not try to clone the atom if it does not exist (Egon Willighagen <egonw@users.sourceforge.net>)
* MDL reading and writing valency (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Line separator fix for RGroup writer (Mark Rijnbeek <mark_rynbeek@users.sf.net>)
* de-Javadoc numerous comments (fixes #2980066) (Carl Masak <cmasak@gmail.com>)
* More extensive testing for removeHydrogens in atomcontainers with hetero atoms without Hs (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Be a bit more forthcoming with debug messages: report also the parameter types of the method (Egon Willighagen <egonw@users.sourceforge.net>)
* This patch makes sure that the removeHydrogens method in AtomContainerManipulator sets hydrogenCoutn to 0 if no hydrogens were on a heavy atom. Till now, this was null, which was at least not good, in a way even wrong. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* converted uses of indexOf to startsWith/contains (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated HIN reader to fix bug 2984581 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed duplication of cloning. (Egon Willighagen <egonw@users.sourceforge.net>)
* 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. (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a typo in the test method name (Egon Willighagen <egonw@users.sourceforge.net>)
* Got rid of some debug prints (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed a regex bug which prevented the engine from properly loading descriptor class names (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Some code cleanup to make it more idiomatic Java (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* New IChemObjectBuilder interface: (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version to indicate this is post 1.3.4 release (Egon Willighagen <egonw@users.sourceforge.net>)
* 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 (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.6
--------
* Updated copyright to 2010 (Egon Willighagen <egonw@users.sourceforge.net>)
* Compare values not objects (fixes #3061263) (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object (Egon Willighagen <egonw@users.sourceforge.net>)
* Smiles parser setting to preserve aromaticity as provided in the Smiles String itself. (Mark Rynbeek <markr@localhost.localdomain>)
* Added two further unit tests: one to see if the descriptor properly 'ignores' hydrogens; a second to reproduce the numbers in the original Wiener paper from 1947 (Egon Willighagen <egonw@users.sourceforge.net>)
* Renabled test which was (accidentally?) outcommented when switching to JUnit4 in commit 06a1a3dd (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a reference to the original Wiener paper (Egon Willighagen <egonw@users.sourceforge.net>)
* No need to declare throws for other Exception's if the superclass is already declared thrown itself (also, no need to define java.lang explicitly) (Egon Willighagen <egonw@users.sourceforge.net>)
* Minor cleanup: corrected copyright statement; simplified JavaDoc by removing empty parameter table (Egon Willighagen <egonw@users.sourceforge.net>)
* Replaced inline citation by reference to the main bibliography (Egon Willighagen <egonw@users.sourceforge.net>)
* Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated javadocs and added extra unit test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Removed output to STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br (Saravanaraj <raj@plantbio.uga.edu>)
* Unit test for bug #3040273. (Saravanaraj <raj@plantbio.uga.edu>)
* Fixed hybridization information: these are sp3 hybridized systems (Egon Willighagen <egonw@users.sourceforge.net>)
* More missing elements for SMILES parsing problems reported in bug #3048501 (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit tests for SMILES parsing bugs reported in #3048501 (Egon Willighagen <egonw@users.sourceforge.net>)
* Upper case the first character to also properly recognize lower cased 'aromatic' two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1 (Egon Willighagen <egonw@users.sourceforge.net>)
* JavaDoc fixes: correct @cdk.cite use, and small typo (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890) (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the maven build file (closes #3042475) (Egon Willighagen <egonw@users.sourceforge.net>)
* a)removed blank/unused methods and fixed imports Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* a)IMatch to Match and constructor call for state used TargetProperties for faster processing Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* a)Assert cleaned and fixed b)Correct ASSERT imports used (Syed Asad Rahman <s9asad@gmail.com>)
* Removed unused code (Syed Asad Rahman <s9asad@gmail.com>)
* Updated checking of indices which now are -1 if unset, instead of null (Syed Asad Rahman <s9asad@gmail.com>)
* a) Default constructor supported as per changes in the CDK b) VFMCS index error should point to -1 not null Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* a)Refactored matchers, atom matcher and bond matcher b)getTanimoto score fixed for single atoms (Syed Asad Rahman <s9asad@gmail.com>)
* Updates for the getImplicitHydrogenCount() renaming (Egon Willighagen <egonw@users.sourceforge.net>)
* The smsd module now depends on the signature module (Egon Willighagen <egonw@users.sourceforge.net>)
* Latest SMSD code 1.2.0: Major changes are: (Syed Asad Rahman <s9asad@gmail.com>)
* Use the factory to not depend on an implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per report #3020065 (Egon Willighagen <egonw@users.sourceforge.net>)
* Introduced a helper class with info about the CDK library: the version number, which is read from the build.props which is now included in the cdk-core.jar (Egon Willighagen <egonw@users.sourceforge.net>)
* Also take into account super classes (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed MDLWriter into MDLV2000Writer (implements #3029447) (Egon Willighagen <egonw@users.sourceforge.net>)
* Assert pattern has the expected value as first argument (Egon Willighagen <egonw@users.sourceforge.net>)
* Use the builder pattern to instantiate an IIsotope (Egon Willighagen <egonw@users.sourceforge.net>)
* MDLV2000 reader interprets D and T without M ISO line mandatory (Mark Rynbeek <markr@localhost.localdomain>)
* Use the PT class to see if something can be an element and removing the redundant element symbol info (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed annotation with TestMethod, not TestClass (fixes #3016632) (Egon Willighagen <egonw@users.sourceforge.net>)
* Skip inner classes for @cdk.module and @cdk.githash JavaDoc tests (fixes #3043084) (Egon Willighagen <egonw@users.sourceforge.net>)
* Throw a CDKException when a QUADRUPLE bond order is in the input, which is not supported by the MDL/Symyx molfile format (fixes #3029352) (Egon Willighagen <egonw@users.sourceforge.net>)
* Deal with a special situation: pyridine N-oxide in the non-charge-separated representation, with a N.sp2.3 nitrogen, with two double bonds. Previously, any ring-outward double bond would disqualify the ring as aromatic. This compound is now an exception. (Egon Willighagen <egonw@users.sourceforge.net>)
* Assert the compound is aromatic (fixes false negative) (Egon Willighagen <egonw@users.sourceforge.net>)
* Exporting the signatures jar (maclean <gilleain.torrance@gmail.com>)
* Removed the OpenJavaDocCheck Jazzy extension which was not supposed to go in; it's not ready for prime time (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies (fixes failing unit tests) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies (fixes failing unit tests) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Release CDK 1.2.6.1 (Egon Willighagen <egonw@users.sourceforge.net>)
* Copy the 2D templates into the source distribution (Egon Willighagen <egonw@users.sourceforge.net>)
* Added finally blocks to MolHandler to close its input streams, with proper logging calls if it fails Fixes bug #3032568 (Jules Kerssemakers <j.kerssemakers@cmbi.ru.nl>)
* UIT timeout fix (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* Cleaned up exception handling in TemplateHandler.loadTemplates() to be more specific and less pessimistic. (Jules Kerssemakers <j.kerssemakers@cmbi.ru.nl>)
* QSAR descriptor values made serializeable (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* Fixed assertion to compare two Vector3d's (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test to assert that two Vector3d's are identical (Egon Willighagen <egonw@users.sourceforge.net>)
* All methods now tested (maclean <gilleain.torrance@gmail.com>)
* Hooking up test machinery (maclean <gilleain.torrance@gmail.com>)
* Altered the getTetrahedralDescription to be get stereo and return ITetrahedralChirality.Stereo (maclean <gilleain.torrance@gmail.com>)
* Moved Stereotool to stereo package (maclean <gilleain.torrance@gmail.com>)
* Convenience method that returns chirality descriptor (R/S) given four atoms in priority order (maclean <gilleain.torrance@gmail.com>)
* Missing docs (maclean <gilleain.torrance@gmail.com>)
* Copyright statements (maclean <gilleain.torrance@gmail.com>)
* Just to be paranoid, test +/- tetrahedra above and below the XY plane (maclean <gilleain.torrance@gmail.com>)
* Tests for square planar shapes, trig bipyr, and oct (maclean <gilleain.torrance@gmail.com>)
* Cleanup and fixing (I think) of the trigonal bipyramidal method (maclean <gilleain.torrance@gmail.com>)
* Test for 3 colinear points (maclean <gilleain.torrance@gmail.com>)
* Better docs (maclean <gilleain.torrance@gmail.com>)
* Tests for tetrahedral sign, some basic defined vectors (maclean <gilleain.torrance@gmail.com>)
* Test class, and name change of distanceToPlane to show that it returns signed (+/-) distance (maclean <gilleain.torrance@gmail.com>)
* Initial go at the StereoTool - functions taken from Jmol's smiles package for 3D stereo checking (maclean <gilleain.torrance@gmail.com>)
* Updated OB note and robustified unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added support for multi-molecule mol2 files. Updated source and added unit test and test file (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated cdk-1.2.x patches for master API (Egon Willighagen <egonw@users.sourceforge.net>)
* Release 1.2.6 (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the DebugBond unit test too now: new DebugBond() has zero atoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Backport patch, to make the patches compile with cdk-1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
* Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. (Egon Willighagen <egonw@users.sourceforge.net>)
* Also fix the new NNBond() == 0 atoms for the nonotify module (Egon Willighagen <egonw@users.sourceforge.net>)
* 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. (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated test to assume new Bond() creates a bond with zero atoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Added two unit tests for aromatic N-oxides that are the basis for failures in SMARTS matching (Rajarshi Guha <rajarshi.guha@gmail.com>)
* added javadoc to IChemObjectReader explaining the split between ISimple and IIterating ChemObjectReaders (Jules Kerssemakers <j.kerssemakers@cmbi.ru.nl>)
* Exceptions when clone atomless ISingleElectron and ILonePair too (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the N.oxide atom type, for structures like (CH3)N=O (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed reading of SD properties: keep the first line too (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed unit test: surely there is no atom with symbol 0... how long has this been failing?? (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated fingerprinter javadoc (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added a test class to aromaticity of three compounds: the last incorrectly fails (Egon Willighagen <egonw@users.sourceforge.net>)
* Also except N.amide as part of an aromatic ring (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test class to repeat atom type perception and test consistency (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up (Egon Willighagen <egonw@users.sourceforge.net>)
* Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then (Egon Willighagen <egonw@users.sourceforge.net>)
* BooleanIOSetting to let MDLWriter output bond type 4 (aromatic) (Mark Rijnbeek <markr@ebi.ac.uk>)
* Reorderd imports (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test cases to check that the code runs when faced with covalently bonded metals. Currenly on failure is due to the presence of Pt, for which we do not have a valency in AtomValence (Rajarshi Guha <rajarshi.guha@gmail.com>)
* chemfilter improvised Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* added ExtAtomContainerManipulator Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* deleted ext Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* updated SMSD code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* updated SMSD code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* Convenience constructors for AtomSignature that take IAtoms rather than atom indices (maclean <gilleain.torrance@gmail.com>)
* Added missing jar meta file for the Signatures library (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated to reflect the upstream jar name (Egon Willighagen <egonw@users.sourceforge.net>)
* Abstract methods not part of API are now protected, to discourage thier use (maclean <gilleain.torrance@gmail.com>)
* Various fixes to tests (maclean <gilleain.torrance@gmail.com>)
* Added the missing assert: runCoverageTest() returns a boolean stating the success (Egon Willighagen <egonw@users.sourceforge.net>)
* cdk.cite references for two Faulon papers (maclean <gilleain.torrance@gmail.com>)
* More missing javadocs - notably the class documentation for AtomSignature and MoleculeSignature (maclean <gilleain.torrance@gmail.com>)
* Mising constructor javadoc, and inheritdoc annotation on AtomSignature (maclean <gilleain.torrance@gmail.com>)
* Final missing test (maclean <gilleain.torrance@gmail.com>)
* Atom signature test methods (maclean <gilleain.torrance@gmail.com>)
* Molecule signature tests (maclean <gilleain.torrance@gmail.com>)
* Signature quotient graph test method (maclean <gilleain.torrance@gmail.com>)
* Missing test for Orbit::iterator (maclean <gilleain.torrance@gmail.com>)
* Removed unused import (Egon Willighagen <egonw@users.sourceforge.net>)
* Molecule From Signature Builder tests (maclean <gilleain.torrance@gmail.com>)
* All orbit methods tested (maclean <gilleain.torrance@gmail.com>)
* Finally correct junit annotations, and sort test (maclean <gilleain.torrance@gmail.com>)
* BeforeClass method must be static; better clone test (maclean <gilleain.torrance@gmail.com>)
* Fixes some problems flagged by PMD (maclean <gilleain.torrance@gmail.com>)
* Use junit's BeforeClass instead of Before annotation (maclean <gilleain.torrance@gmail.com>)
* Added missing githash tags, to add links in the JavaDoc to the source code repository (Egon Willighagen <egonw@users.sourceforge.net>)
* Inherit JavaDoc where methods overwrite a super method (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed PMD warnings: more descriptive field names; use of Integer.valueOf() (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test method annotation for the clone() method (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed some unnecessary imports (maclean <gilleain.torrance@gmail.com>)
* Test orbit cloning (maclean <gilleain.torrance@gmail.com>)
* Improved canonical label method in graph signature (maclean <gilleain.torrance@gmail.com>)
* Integer invariants, and updated signatures jarfile (maclean <gilleain.torrance@gmail.com>)
* Added JavaDoc HTML generation for the signature module (Egon Willighagen <egonw@users.sourceforge.net>)
* Hooked in PMD testing for the signature module (Egon Willighagen <egonw@users.sourceforge.net>)
* Defined dependencies for the test module (Egon Willighagen <egonw@users.sourceforge.net>)
* Hooked the signature module into the CDK build system (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed the dependency on the nonotify module (Egon Willighagen <egonw@users.sourceforge.net>)
* Created a CDK style module test suite (Egon Willighagen <egonw@users.sourceforge.net>)
* MoleculeFromSignatureBuilder tests (maclean <gilleain.torrance@gmail.com>)
* Extend from CDKTestCase and use the slow running test check (maclean <gilleain.torrance@gmail.com>)
* Fixed and cleaned up molecule signature tests (maclean <gilleain.torrance@gmail.com>)
* Initial commit of signature package (maclean <gilleain.torrance@gmail.com>)
* Added OpenJavaDocCheck 0.5 - the Jazzy spell checking extension (Egon Willighagen <egonw@users.sourceforge.net>)
* specify fail behavior (returns null) in javadoc (jonalv <jonathan.alvarsson@gmail.com>)
* Added PMD tests for detecting misuse of TestClass and TestMethod, e.g. TestClass on a method. (fixes #3014808) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed two lines added in master to the removed doccheck target (Egon Willighagen <egonw@users.sourceforge.net>)
* Improved javadoc generation using a link tag, so that references to java library classes are resolved properly (maclean <gilleain.torrance@gmail.com>)
* Update OpenJavaDocCheck to 0.5: fixing a few false positives (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed use of the proprietary DocCheck utility (Egon Willighagen <egonw@users.sourceforge.net>)
* OpenJavaDocCheck errors are fixed for SMSD related modules Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* solved cdk-Bugs-3006773 : small JavaDoc errors in the smsd module (Syed Asad Rahman <s9asad@gmail.com>)
* Fix for character spacing for "APO" line in RGFile output (Mark Rynbeek <markr@localhost.localdomain>)
* Branch open for commits for the future 1.3.6 (Egon Willighagen <egonw@users.sourceforge.net>)
* Use the new tests in more situations (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.7
--------
* Replaced the broken links with new ones (fixes #3108471) (Egon Willighagen <egonw@users.sourceforge.net>)
* Upgraded to the final JNI-InChI 0.7: (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed test class to conform the expected naming pattern (Egon Willighagen <egonw@users.sourceforge.net>)
* Factored out a AbstractCDKObjectTest now used in AbstractAtomParity test, to add the missing unit test (Egon Willighagen <egonw@users.sourceforge.net>)
* Overwrite the default public constructor because this class is not supposed to be instantiated. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit test (Egon Willighagen <egonw@users.sourceforge.net>)
* Strongly typed the comparator, removing no longer valid tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed an obsolete test (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed unit test: test the correct class (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed methods according to naming coverage testing naming scheme (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing classificatins to some descriptors (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Use a builder more efficiently (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing sulphur atom type as found in thiosulphonate (fixes #3080848) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added acidic and basic group count descriptors (implements #3056330) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing atom type: positively charged P with three neighbors, of which one double bonded (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a unit test for the C=[N+]=[N-] functional group (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated string generation for molecular formulae that address bug 3071473 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug 2871303, which appears to be resolved now (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit test for bug 2853035, which appears to be resolved now (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit test for bug 3001616, which appears to be resolved now (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Overwrite tests from AbstractChemObject to ensure that no change events are thrown when properties are changed, which was fixed in June in patch 2fe119c3a874dabb9bfb66ea2adbaaa6b2e6ed5d (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed merge artefact (Egon Willighagen <egonw@users.sourceforge.net>)
* test for streams returning false on ready() (vedina <jeliazkova.nina@gmail.com>)
* Revert "Updated isotope to have proper equals and hashCode methods" (Egon Willighagen <egonw@users.sourceforge.net>)
* Revert "Updated molecular formula to use the new equals method from Isotope. This methods checks for equality of two instances using symbol, mass num, exact mass and natural abundance" (Egon Willighagen <egonw@users.sourceforge.net>)
* Revert "Updated MF manipulator to properly evaluate total mass and generate formula string correctly, even when there are multiple isotopes of the same element. Added unit test. Simplified molecular formula to properly use the isotopes map as an actual map" (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated Javadocs, since Egon is a nice guy :) (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Actually put in a test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Implementation of the Fmf descriptor described by Yang et al, J Med Chem, 2010. The descriptor is described i in Yang et al, J Med Chem 2010, and is an approach to characterizing molecular complexity based on the Murcko framework (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated MF manipulator to properly evaluate total mass and generate formula string correctly, even when there are multiple isotopes of the same element. Added unit test. Simplified molecular formula to properly use the isotopes map as an actual map (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated molecular formula to use the new equals method from Isotope. This methods checks for equality of two instances using symbol, mass num, exact mass and natural abundance (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated isotope to have proper equals and hashCode methods (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit test and test file for bug 2917084 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added coverage testing for constructors (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed the CDKSourceCodeWrite to create compilable source code (Egon Willighagen <egonw@users.sourceforge.net>)
* Added use of Groovy to test if the output compiles (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated Murcko code so that we save the appropriatley cloned framework. Also updated unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added missing entry for compiling the iordf module (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated for API changes in the IChemObjectBuilder (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated for API change for get/setImplicitHydrogens() (Egon Willighagen <egonw@users.sourceforge.net>)
* Copied the inchi module into the sinchi module, providing Standard InChI support with JNI-InChI 0.7. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added iordf to the ojdcheck target (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies for the test module for iordf (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing JavaDoc for the iordf module (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing JavaDoc (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a PMD warning: too short variable name (Egon Willighagen <egonw@users.sourceforge.net>)
* Reduced complexity by introducing two maps (Egon Willighagen <egonw@users.sourceforge.net>)
* Prefixed the hybridization constants with HYBRID_ (Egon Willighagen <egonw@users.sourceforge.net>)
* Made final static full upper case, as requested by PMD (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed output to STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Added iordf to dist-large (Egon Willighagen <egonw@users.sourceforge.net>)
* Added (de)serialization of the IPseudoAtom fields to RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added (de)serialization of the IElectronContainer fields to RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added (de)serialization of the IIsotope fields to RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a few missing dependencies (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed module allocation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtripping for IAtomType.formalCharge (Egon Willighagen <egonw@users.sourceforge.net>)
* Hooked in testing for iordf (Egon Willighagen <egonw@users.sourceforge.net>)
* Reuse of earlier extracted helper methods (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtripping of IAtom.atomtypeName and .maxBondOrder (Egon Willighagen <egonw@users.sourceforge.net>)
* Test all bond types (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtrip of IElement.atomicNumber and IAtomType.hybridization (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtrip of IChemObject.identifier (Egon Willighagen <egonw@users.sourceforge.net>)
* Added read and write of IBond and .order (Egon Willighagen <egonw@users.sourceforge.net>)
* Added class JavaDoc (Egon Willighagen <egonw@users.sourceforge.net>)
* Added method to create identifiers based on the hashCode (Egon Willighagen <egonw@users.sourceforge.net>)
* Added read/write of IAtom.symbol in RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a Java API version of the CDK ontology (not synched to the OWL) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added reader and writer for the CDKOWL/N3 format (Egon Willighagen <egonw@users.sourceforge.net>)
* Added framework to convert the CDK data model into a JEna Model (Egon Willighagen <egonw@users.sourceforge.net>)
* Defined a new format, serializing the CDK data model into the Web Ontology Language (OWL) in the Notation3 (N3) format. (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version to indicate it is the development version (Egon Willighagen <egonw@users.sourceforge.net>)
* Throw a change event when an existing property is removed (fixes #2993561). (Egon Willighagen <egonw@users.sourceforge.net>)
* Do no pass stereo information when none (null) was read (Egon Willighagen <egonw@users.sourceforge.net>)
* Three fixes: extended the JavaDoc, reset the isInterrupted boolean when an interruption occured, and marked how interruption should be used (which means sequential calls, not parallel) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added testing of the isOK() method (Egon Willighagen <egonw@users.sourceforge.net>)
* Because the DeduceBondSystemTool does not consider rings with more than 7 atoms, we can speed up ring finding by setting the (new) maxRingSize parameter (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a constructor to set a custom ring finder instance (e.g. with a time out set) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added build/*.javafiles to the .classpath so that the coverage unit tests succeed in Eclipse (Egon Willighagen <egonw@users.sourceforge.net>)
* modified to avoid InputStreamReader.ready() method (vedina <jeliazkova.nina@gmail.com>)
* Added unit tests for bug 3088164 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated to ensure that we properly handle tag separator lines that may not be completely empty (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed bug in reading a SDF property whose value is a single space (Rajarshi Guha <rajarshi.guha@gmail.com>)
* removed debug code and add another check in the unit test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added another unit test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* New package for fragmentation algorithms - currently exhaustive and Murcko. Added unit tests and updated code to use the new Murcko fragmenters. Removed old murcko fragmenter which was unmaintainable. Additional unit tests have been added and Javadocs have been improved (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added new test method for aromatic bonds (Egon Willighagen <egonw@users.sourceforge.net>)
* Build molecules with aromatic bonds if labelled with 'p' (maclean <gilleain.torrance@gmail.com>)
* Aromatic bond (output) support for signatures (maclean <gilleain.torrance@gmail.com>)
* - MDLReader.java AtomAtomMapping property set as String instead of Integer (unknown <Gott@.(none)>)
* Added a 'reader' for MoSS output files, which reads the given substructures as IMolecule's, as we do not have a proper data model for query structures yet (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a format definition for the output of the MoSS software (Egon Willighagen <egonw@users.sourceforge.net>)
* Check for a null major isotope, which happens with R-groups (maclean <gilleain.torrance@gmail.com>)
* Small typo fix to point to the correct test class (Egon Willighagen <egonw@users.sourceforge.net>)
* Four unit tests that test if the fingerprint calculation is affected by atom or bond permutation (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated version and confirmed inception year (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated getVersion method to not print to stdout (Rajarshi  Guha <rajarshi.guha@gmail.com>)

1.3.8
--------
* Updated the changelog (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the README (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version for release 1.3.8 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added description of IO settings to the writers JavaDoc (fixes #3029445) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Changed method names to versions expected by the coverage testing system (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing test annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed returning the monomer names when no strands are defined (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed counting the number of monomers when no strands are defined (Egon Willighagen <egonw@users.sourceforge.net>)
* Restored the previous behavior of a zero default charge, fixing very many unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved packaging of the PeriodicTable data to the new model too (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated Atom(String) constructor to call the Atom(Element) constructor, so that even if we instantiate an atom just by symbol we still get an atomic number. Needed to update the Element constructor to accept Integer (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Moved the test classes from the standard to the core TestSuite too (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated module assignments (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit tests for H-bond donor/acceptor for bug #3133610 (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed typo in JavaDoc (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed isotope class to get the proper isotope if mass number is available, rather than using the major isotope by default (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added some documentation for possibly non-obvious methods (Rajarshi Guha <rajarshi.guha@gmail.com>)
* AminoAcidCountDescriptor constructor made thread safe (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* System.out.println() removed in ProtonTotalPartialChargeDescriptor.java (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* Added missing copyright/license and cdk.module statements (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing JavaDoc and unit tests for VisitedAtoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a simple code example for how to use the CIPTool (Egon Willighagen <egonw@users.sourceforge.net>)
* Made a few classes private to the package (Egon Willighagen <egonw@users.sourceforge.net>)
* Added comment in JavaDoc about the sorted nature of the method input (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for aromatic molecular signatures (Egon Willighagen <egonw@users.sourceforge.net>)
* Added testing of bromochlorofluoroiodomethane (Egon Willighagen <egonw@users.sourceforge.net>)
* Only consider recursion if all ligand atoms are identical and equal in number (fixes R detection in PubChem CID 42475007) (Egon Willighagen <egonw@users.sourceforge.net>)
* Keep track of which atoms have already been visited, to properly terminate when we give up (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests to uncover a non-termination issue in the CIP algorithm reported by Ola (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test to make sure no chirality is detected for the FC(Me)(Me)R carbon (Egon Willighagen <egonw@users.sourceforge.net>)
* Test case for another termination problem: the previous 'fix' broke the proper ordering of ligands when there is more than one, IAOI one ligand count was only 1 (thanx to Gilleain for spotting this) (Egon Willighagen <egonw@users.sourceforge.net>)
* Test case provided by Gilleain around termination, using the SMILES as input (Egon Willighagen <egonw@users.sourceforge.net>)
* Set up a CIP module. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @TestMethod annotation for LoggingTool (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Converted all readers to the new read() API (Egon Willighagen <egonw@users.sourceforge.net>)
* Branch open for 1.3.8 patches (Egon Willighagen <egonw@users.sourceforge.net>)
* Compile fixes caused by rebasing artefacts as some modules still change bits in order modules (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored reaction boxes into a IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored foreground color into a IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored showIm/ExplicitHydrogens as IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Using IRenderer<T> interface instead of implementation (maclean <gilleain.torrance@gmail.com>)
* More types in renderers, and associations between renderers (maclean <gilleain.torrance@gmail.com>)
* Point to the interfaces rather than the implementation (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Yeah, the last fix. The 'render' module is now PMD, JUnit4, and JavaDoc clean (Egon Willighagen <egon.willighagen@gmail.com>)
* More JavaDoc and PMD fixes: removed an unused parameter, throws non-generic exception, fixed JavaDoc errors and added missing JavaDoc (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed some PMD warnings: longer variable names (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed a NPE: if the atom does not have a atomic number defined, return the default color (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing unit tests and matching annotation for the render module (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a few missing test methods for the RendererModel (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing TestClass/-Method annotations and test methods for the default colors (Egon Willighagen <egon.willighagen@gmail.com>)
* JavaDoc updates: added missing bits (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing dependency of test-render on annotation (Egon Willighagen <egon.willighagen@gmail.com>)
* Report the unregistered parameter class name (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed getting the default value of a parameter: do not reuse getParameter() but use some local logic to instantiate a new instance if needed (Egon Willighagen <egon.willighagen@gmail.com>)
* Added the RendererModel.get(paramType) convenience method (Egon Willighagen <egon.willighagen@gmail.com>)
* Renamed get/setRenderingParameter methods to shorter names (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Throw an exception when a parameter value is requested, but not set yet by registering the appropriate generator (Egon Willighagen <egon.willighagen@gmail.com>)
* Added getDefaultRenderingParameter convience method, using generics powers (Egon Willighagen <egon.willighagen@gmail.com>)
* Added setRenderingParameter convenience method, using generics powers (Arvid Berg <goglepox@users.sourceforge.net>)
* Removed obsolete RenderingPatameters class (Egon Willighagen <egon.willighagen@gmail.com>)
* Changed wedge width to rendering parameter (maclean <gilleain.torrance@gmail.com>)
* Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved ExternalHighlightColor into RendererModel for now, to solve a compile dependency (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted hoverOverColor to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted externalHighlightColor to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted mappingColor and mappingLineWidth to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted boundsColor to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed returning of the actual paramater value, instead of a new instance all the time: getClass().getClass() != getClass() (Egon Willighagen <egon.willighagen@gmail.com>)
* Unit test for returning the parameter value, instead of a new instance all the time (Egon Willighagen <egon.willighagen@gmail.com>)
* Removed to unused imports (Egon Willighagen <egon.willighagen@gmail.com>)
* Split up the old IGenerator interface into IGenerator and IAtomContainerGenerator, the first now only containing the method for getting the parameters (Egon Willighagen <egon.willighagen@gmail.com>)
* Factored out a ColorHash IRenderingParamater (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted BondDistance into an IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted FontName and FontStyle into IGeneratorParameters (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted useAntiAliasing into a IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted ringProportion to IGeneratorParameter variants (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted showAromaticity and cdkStyleAromaticity to IGeneratorParameter variants (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted bondWidth and defaultBondColor into IGeneratorParameter's (Egon Willighagen <egon.willighagen@gmail.com>)
* Removed last four rendering parameters from BasicAtomGenerator: isCompact, compactShape, isKekule, and showEndCarbons (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved the atom radius into the new rendering parameter API (renderbasic module) (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved rendering parameters for atom draw colors to the new IGeneratorParameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a method to list all rendering parameters know to the current renderer (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing @cdk.githash tags (Egon Willighagen <egon.willighagen@gmail.com>)
* The default atom color is white, not black, according to the implementation (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed a null pointer exception: return the default color, if the atom has no charge (Egon Willighagen <egon.willighagen@gmail.com>)
* Updated test: apparently, the values for Color.PINK can change between JVM releases? (Egon Willighagen <egon.willighagen@gmail.com>)
* Made method public static, as expected by the JUnit framework (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted margin into the RenderingParameter variant (Egon Willighagen <egon.willighagen@gmail.com>)
* Changed generic definition (Arvid Berg <goglepox@users.sourceforge.net>)
* Moved the atom radius into the new rendering parameter API (render module) (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved rendering parameters for atom draw colors to the new IGeneratorParameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Set up a API to retrieve a IRenderingParameter from the RenderModel (Egon Willighagen <egon.willighagen@gmail.com>)
* Return the default if the value has not been overwritten with setValue() (Scooter Morris <scooter@cgl.ucsf.edu>)
* Changed getParameters() to use IGeneratorParameter<?> (Arvid Berg <goglepox@users.sourceforge.net>)
* Applied Arvids suggestions: use generics instead of Object; also now provides an abstract default class which IGeneratorParameter implementation can inherit for the basic get/set functionality (Egon Willighagen <egon.willighagen@gmail.com>)
* Added an IGeneratorParameter interface, to tie parameters to the modules to which they apply. Parameters *can* be reused, by following the rendering module dependencies. (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing JavaDoc to render interfaces (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing JavaDoc for getColor() methods (Egon Willighagen <egon.willighagen@gmail.com>)
* Added IRenderer methods needed for the Controllers. (Egon Willighagen <egon.willighagen@gmail.com>)
* Introducing IRenderer, to solve some dependencies (Egon Willighagen <egon.willighagen@gmail.com>)
* Setting up the new render infrastructure. (Egon Willighagen <egon.willighagen@gmail.com>)