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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>)