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changelog.txt
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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 <[email protected]>)
* Capability to read and write reaction properties information. Added theirs corresponding tests (Miguel Rojas Cherto <[email protected]>)
* Fixed serialization of IAtom's with null formal charge to not cause NullPointerExceptions (Egon Willighagen <[email protected]>)
* Added unit test for serialization of null formal charges into the MDL molfile format (which currently fails) (Egon Willighagen <[email protected]>)
* Fixed a typo from the previous merge (Rajarshi Guha <[email protected]>)
* Updated Javadocs for SMARTS query tool to indicate unsupported features (Rajarshi Guha <[email protected]>)
* Cleaned up source file to remove spurious line endings (Rajarshi Guha <[email protected]>)
* Bumped version number (Egon Willighagen <[email protected]>)
* The formal charge of the IAtomcontainer is transfered to IMolecularFormula (Miguel Rojas Cherto <[email protected]>)
* Fixed bug 2787332 The old bond array in the gasteiger charge calculation was set to the wrong size (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Added new taglet to process cdk.githash tag and link Javadocs to sources in Git repo (Rajarshi Guha <[email protected]>)
* Updated cdk.svnrev tags to cdk.githash tags (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Removed obsolete renderer code: either use cdk-1.0.x or jchempaint-primary (Egon Willighagen <[email protected]>)
* Added test for bug 2786624 in the parser test suite (Rajarshi Guha <[email protected]>)
* Added links to PMD pages (Egon Willighagen <[email protected]>)
* Added link to JUnit stats (Egon Willighagen <[email protected]>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Updated version number (Egon Willighagen <[email protected]>)
* Added test to ensure IAtomContainers are not sneaked in via IMoleculeSet.add(IAtomContainerSet) (Egon Willighagen <[email protected]>)
* Overwritten addAtomContainer(IAtomContainer, double) too, to throw an IllegalArgumentException when a non-IMolecule is passed (Egon Willighagen <[email protected]>)
* Now throws an IllegalArgumentException when it is tried to store an IAtomContainer which is not an IMolecule (Egon Willighagen <[email protected]>)
* Added unit test for #2784182 (Egon Willighagen <[email protected]>)
* new test with reserpine (Stefan Kuhn <[email protected]>)
* Added taglets for threading safety (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added unit test for bug #2784209 which currently fails (Egon Willighagen <[email protected]>)
* More removal of explicit org.openscience.cdk package names: throws clauses (Egon Willighagen <[email protected]>)
* More removal of explicit org.openscience.cdk package names (Egon Willighagen <[email protected]>)
* More removal of explicit org.openscience.cdk package names: for new org.openscience.cdk.Foo() calls (Egon Willighagen <[email protected]>)
* Removed explicit org.openscience.cdk.interfaces packages names (fixes #2783549) (Egon Willighagen <[email protected]>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the datadebug module (fixes #2783549) (Egon Willighagen <[email protected]>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the data module (fixes #2783549) (Egon Willighagen <[email protected]>)
* breakout of recursion option on AllRingsFinder (mark_rynbeek <[email protected]>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <[email protected]>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <[email protected]>)
* Controller of the mass when it is out of the range (Miguel Rojas Cherto <[email protected]>)
* 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 <[email protected]>)
* Moved the pubchem fingerprinter to the fingerprinter module, since it needs SMARTS which is not a dependency of the standard module (Rajarshi Guha <[email protected]>)
* Added more test cases comparing our FP's with those provided by Pubchem (Rajarshi Guha <[email protected]>)
* Updated Javadocs, cleaned up some tests (Rajarshi Guha <[email protected]>)
* Added test for benzene (Rajarshi Guha <[email protected]>)
* Updated SMARTS patterns to use H count specifications rather than explicit H matches (Rajarshi Guha <[email protected]>)
* Initial version of Pubchem fingerprints based on the public domain NCGC code. Includes unit tests (Rajarshi Guha <[email protected]>)
* Updated to intelligently add H's to a PLANAR3 N, fixes bug 2781199 (Rajarshi Guha <[email protected]>)
* Added test case for bug 2781199 (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* removed needless white space (Rajarshi Guha <[email protected]>)
* Refactored to provide a query container specifically for pharmacophore queries. (Rajarshi Guha <[email protected]>)
* Updated the toString tests (Rajarshi Guha <[email protected]>)
* Added test methods for the new toString methods. Also added test method annotations (Rajarshi Guha <[email protected]>)
* provided toString methods for the pcore query classes (Rajarshi Guha <[email protected]>)
* Added a unit test to ensure SD fields are read for all molecules (Egon Willighagen <[email protected]>)
* Added unit test for bug 1579235, which checks for aromaticity in indolizine (Rajarshi Guha <[email protected]>)
* Updated code to use 1.5 idioms and remove use of Iterator (Rajarshi Guha <[email protected]>)
* Added links to PMD pages (Egon Willighagen <[email protected]>)
* Added link to JUnit stats (Egon Willighagen <[email protected]>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Updated build system to take into account non public classes as well. Also updated ChiIndexUtils to be package private (Rajarshi Guha <[email protected]>)
* split up test (Stefan Kuhn <[email protected]>)
* new files (Stefan Kuhn <[email protected]>)
* more tests for cml reading (Stefan Kuhn <[email protected]>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <[email protected]>)
* Fixed cast, remove redundant full package name (Egon Willighagen <[email protected]>)
* Added unit test for #2692107 (Egon Willighagen <[email protected]>)
* Fixed typo: missing 's' (Egon Willighagen <[email protected]>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <[email protected]>)
* Fixed cast, remove redundant full package name (Egon Willighagen <[email protected]>)
* Added unit test for #2692107 (Egon Willighagen <[email protected]>)
* Fixed typo: missing 's' (Egon Willighagen <[email protected]>)
* Use the proper folder name, including the CDK version (Egon Willighagen <[email protected]>)
* 1.2.1 release being prepared (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Fixed bug 2729120 and added unit test (Rajarshi Guha <[email protected]>)
* Updated comment to fix bug 2768643. (Rajarshi Guha <[email protected]>)
* Partial fix for bug 2719237. Made getBondOrderSum static, added unit test for it (Rajarshi Guha <[email protected]>)
* Typo: proteinl -> protein (Egon Willighagen <[email protected]>)
* Made class public, to unbreak adding it to the build/*.javafiles (Egon Willighagen <[email protected]>)
* Partially fixed SMARTS matching for R0. Updated target molecule initialization to explicitly (Rajarshi Guha <[email protected]>)
* Fixed dubious equality test. A private method was checking Double objects via reference. (Rajarshi Guha <[email protected]>)
* Added test method annotation. Completes coverage for data module (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Code cleanup of ChiIndexUtils. Converted to 1.5 idioms (Rajarshi Guha <[email protected]>)
* Clean up of PathTools and added test method annotation, so that core is completely covered (Rajarshi Guha <[email protected]>)
* Fixed the previous commit to edit the cdk.keyword line, not the cdk.module line (Egon Willighagen <[email protected]>)
* More consistent keywords used (Egon Willighagen <[email protected]>)
* Added a test to ensure that Integer objects are compared by value rather than reference (Rajarshi Guha <[email protected]>)
* Added a test case to check that atom container diffs are correct when using deserialized objects (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics, one last time... Leander should work by now... (Egon Willighagen <[email protected]>)
* Use interface instead of implementation (Egon Willighagen <[email protected]>)
* Some other code cleanup (Egon Willighagen <[email protected]>)
* Added generics, here too (Egon Willighagen <[email protected]>)
* Added generics, here too (Egon Willighagen <[email protected]>)
* Use interface instead of implementation (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Removed an unused import (Egon Willighagen <[email protected]>)
* Use IAtomContainer instead of IMolecule, as the actual matching is using IAtomContainers already (fixes #2686249) (Egon Willighagen <[email protected]>)
* Fixed a ClassCastException (fixes #2685134) (Egon Willighagen <[email protected]>)
* Added source attrib to fix building the Ubuntu .deb (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Removed libdepends include for test-ioformats, which does not actually have libdepends (Egon Willighagen <[email protected]>)
* Updated so that if a target atom has no symbol (such as pseudo atoms) the match returns false (rather than an NPE) (Rajarshi Guha <[email protected]>)
* Fixed proper handling of #n SMARTS querys (Rajarshi Guha <[email protected]>)
* Added test case for bug 2686473 (Rajarshi Guha <[email protected]>)
* Added note on Ant 1.7.1 required (Egon Willighagen <[email protected]>)
* Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness (Egon Willighagen <[email protected]>)
* Added a missing dep (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Fixed duplicate storage of layout templates, which only belong in the sdg module, not extra module too (Egon Willighagen <[email protected]>)
* used interfaces where possible and updated to 1.5 idioms (Rajarshi Guha <[email protected]>)
* Updated to use interfaces where possible and cleaned up code to use 1.5 idioms (Rajarshi Guha <[email protected]>)
* Added unit test for a ONS Solubility solute, which fails to be parsed when RDF. But does not fail here. (egonw <[email protected]>)
* Export the jniinchi lib (Egon Willighagen <[email protected]>)
* Fixed a few test class instantiation problems (Egon Willighagen <[email protected]>)
* Fixed constructor: wrong file format; add getClassLoader() (Egon Willighagen <[email protected]>)
* Fixed for NewCDKTestCase -> CDKTestCase renaming (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
1.3.1
-----------
* Bumped version for 1.3.1 release (Egon Willighagen <[email protected]>)
* Added some extra lines, hopefully fixing the conflicts all the time (Egon Willighagen <[email protected]>)
* Fixed param name (Egon Willighagen <[email protected]>)
* Updated the makefp3d target to work with the current build system (Egon Willighagen <[email protected]>)
* Set up a branch for the 1.2.4 release (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added tests to match hydrogens (mark_rynbeek <[email protected]>)
* Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator (Uli Köhler <[email protected]>)
* Reworked the tests for bug 2898032. Updated Javadocs for smiles generator (Rajarshi Guha <[email protected]>)
* Added unit test to confirm and check for bug 2898032 (Rajarshi Guha <[email protected]>)
* Fixed junior issue 1802586: Misuse of assertTrue for tested strings (Uli Köhler <[email protected]>)
* Made the AtomContainerPermutors IAtomContainer implementation independent (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch (Egon Willighagen <[email protected]>)
* Implemented instantiating custom loggers; example in the unit test class (Egon Willighagen <[email protected]>)
* Added the use of the SystemOutLoggingTool as back up (Egon Willighagen <[email protected]>)
* Added a ILoggerTool implementation for STDOUT (Egon Willighagen <[email protected]>)
* Dig up and updated the copyright history (Egon Willighagen <[email protected]>)
* Factored out initialization of the tool, to allow reusing the code for other logger class names (Egon Willighagen <[email protected]>)
* Moved the log4j.jar depending LoggingTool into a separate module (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added generation of java source jars (Peter Odéus <[email protected]>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <[email protected]>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <[email protected]>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <[email protected]>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <[email protected]>)
* Added reading of E/Z stereochemistry from double bonds in MDL V2000 molfiles. (Egon Willighagen <[email protected]>)
* A minor fix to clean up a PDMD warning (Rajarshi Guha <[email protected]>)
* Overwrite unit tests, because there are no change events passed around at all for the NoNotification interface implementations (Egon Willighagen <[email protected]>)
* Added missing unit tests for IChemModel event propagation for the ICrystal field (Egon Willighagen <[email protected]>)
* Fixed propagation of change events to IChemModel when modifications are made in child IChemObjects (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Synchronized with the Blue Obelisk version (Egon Willighagen <[email protected]>)
* Added unit test to the function of the new IO setting to force 2D coordinate output. (Egon Willighagen <[email protected]>)
* Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted. (Egon Willighagen <[email protected]>)
* Added unit test to verify that if 2D and 3D coordinates are available, the 3D coordinates are outputted. (Egon Willighagen <[email protected]>)
* Changed IBond.get/setStereo() to use a IBond.Stereo enumeration instead of an int (fixes #2855850): (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added the Mannhold LogP descriptor (Egon Willighagen <[email protected]>)
* Added the Mannhold LogP descriptor to the ontology (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Fixes ClassCastException when not IMolecule (Arvid Berg <[email protected]>)
* Upgraded to PMD 2.4.5 with many bug fixes, giving more accurate error reports (Egon Willighagen <[email protected]>)
* Added missing dependency on cdk-diff, being used in one of the unit tests (Egon Willighagen <[email protected]>)
* Fixed methods names to match those in the test class (Egon Willighagen <[email protected]>)
* Fixed test method name to match the expected patters, fixing a coverage test fail (Egon Willighagen <[email protected]>)
* Removed duplicate code: MolecularFormulaTest now extends AbstractMolecularFormulaTest (Egon Willighagen <[email protected]>)
* Fixed test method annotation to point to the right method (Egon Willighagen <[email protected]>)
* Added missing @TestMethod annotation (Egon Willighagen <[email protected]>)
* Added modules that were missing from the PMD testing (Egon Willighagen <[email protected]>)
* Added modules that were missing from the doccheck testing (Egon Willighagen <[email protected]>)
* Added reference to IUPAC documentation about stereochemistry visualization. (Stefan Kuhn <[email protected]>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <[email protected]>)
* Added missing dependency introduced by the use of AbstractFingerprinterTest in test-standard. (Egon Willighagen <[email protected]>)
* Updated the unit test classes for all IFingerprinter implementations to use the new AbstractFingerprinter class; a few unit tests actually fail (Egon Willighagen <[email protected]>)
* Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations (Egon Willighagen <[email protected]>)
* Clean up of layout. (Jonathan Alversson <[email protected]>)
* 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 <[email protected]>)
* Added missing dependencies (Egon Willighagen <[email protected]>)
* Added ioformats to modules to test (Egon Willighagen <[email protected]>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where multiline field data is found. (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Factored out steps in reading the SD file data block (Egon Willighagen <[email protected]>)
* Bumped version, to make it clear this is not the 1.2.3 release (Egon Willighagen <[email protected]>)
* Bumped version, to make it clear this is not the 1.3.0 release (Egon Willighagen <[email protected]>)
* Fixed registering on the cdk.threadnonsage tag (closes #2796362) (Egon Willighagen <[email protected]>)
* Removed obsolete pattern from old svnrev tag (Egon Willighagen <[email protected]>)
* Fixed JavaDoc to remove traces of the old svnrev Tag (Egon Willighagen <[email protected]>)
* Synchronized exception message with implementation (fixes #2844333) (Egon Willighagen <[email protected]>)
* Made class private again, per authors request (Egon Willighagen <[email protected]>)
* Any class will do, not just public, final and abstract (Egon Willighagen <[email protected]>)
* Two further compile fixes after the merge with CDK 1.2.x (Egon Willighagen <[email protected]>)
* Made the class public, to fix a compile problem introduced by the merge with CDK 1.2.x (Egon Willighagen <[email protected]>)
* Added ant task to calculate JavaNCSS code statistics (Egon Willighagen <[email protected]>)
* Added JavaNCSS 32.53 (LGPL 3.0) (Egon Willighagen <[email protected]>)
* The Pauling Electronegativity is copied in configure as well. I can't see why not copy everything we have. (Stefan Kuhn <[email protected]>)
* Revert "added a test for bug 2831420": (Egon Willighagen <[email protected]>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <[email protected]>)
* added a test for bug 2831420 (Stefan Kuhn <[email protected]>)
* added a test for bug #2831420 (Stefan Kuhn <[email protected]>)
* Made InChIGeneratorFactory a singleton. (jonalv <[email protected]>)
* Layout. (jonalv <[email protected]>)
* Added bug annotation (Rajarshi Guha <[email protected]>)
* test case for bug #2846213 (Stefan Kuhn <[email protected]>)
* Fixed perception of N.planar3 where N.sp2 was detected, by now taking into account the given hydrogen count. (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added assertions to unit test for values being not null (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* Unsealed the XOM jar to allow having the CustomSerializer (Egon Willighagen <[email protected]>)
* Fixed Javadocs error (Rajarshi Guha <[email protected]>)
* Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag (Rajarshi Guha <[email protected]>)
* Added support for 'public enum's (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* added a new test for bondtools (Stefan Kuhn <[email protected]>)
* Fixed inconsistency between accepts() and write: also support writing of IAtomContainerSet and IAtomContainer as accepts() indicates (fixes #2827745) (Egon Willighagen <[email protected]>)
* General test for testing consistency between write() and accepts(), testing that all accepted IChemObject's can also be written (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Remove erroneous throws statement (Egon Willighagen <[email protected]>)
* Bug found calculating the exact mass given a molecular formula when it is negative charged. (Miguel Rojas Cherto <[email protected]>)
* Fixed reading of the cdk/dict/data/elements.owl database which is now in OWL (Egon Willighagen <[email protected]>)
* Fixed issue 2458210: use assertNotNull(foo) etc instead of assertTrue(foo != null). (Uli Köhler <[email protected]>)
* Added minimum equivalents for BondManipulator.getMaximumBondOrder() methods (Egon Willighagen <[email protected]>)
* Fixes asserts: after removal *no* change should be recorded (Egon Willighagen <[email protected]>)
* Added IO option to disable generator of XML declaration statements in the output CML. (Egon Willighagen <[email protected]>)
* Added generics, and consistified code by always returning a List<?> of the same '?'. (And some 80 chars fixes in the JavaDocs.) (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added unit tests for event propagation from [Molecule|Reaction|Ring]Sets to ChemModel. (Egon Willighagen <[email protected]>)
* More testing of flags. (Egon Willighagen <[email protected]>)
* Fix for junior job id: [ 1837692 ] Test methods should throw only one Exception. (Paul Turner <[email protected]>)
* Fixed missing imports and wrapped to 80 chars (Egon Willighagen <[email protected]>)
* Better excpetion handling in builder3d: (Stefan Kuhn <[email protected]>)
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 [email protected]
* 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 <[email protected]>)
* More unit tests for the MCSS problem in bug report 2944080. (Egon Willighagen <[email protected]>)
* Simplified the code using the new 'T read(T)' API used in MDLV2000Reader as defined by the ISimpleChemObjectReader (Egon Willighagen <[email protected]>)
* Updated for the new generics 'T read(T)' API in ISimpleChemObjectReader. (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added missing dependency, fixing the unit test reading a file from data/ (Egon Willighagen <[email protected]>)
* added working implementations for PartialFilledStructureMerger and CrossoverMachine (Stefan Kuhn <[email protected]>)
* added working implementations for PartialFilledStructureMerger and CrossoverMachine (Stefan Kuhn <[email protected]>)
* tests for crossover machine and PartialFilledStructureMerger (Stefan Kuhn <[email protected]>)
* tests for crossover machine and PartialFilledStructureMerger (Stefan Kuhn <[email protected]>)
* added dependency (Stefan Kuhn <[email protected]>)
* Fixed use of global isRef variable, to make it threading-safe (Egon Willighagen <[email protected]>)
* Added control 'isref' creating a CML with reaction and listmolecules (Miguel Rojas Cherto <[email protected]>)
* Removed unused import (Egon Willighagen <[email protected]>)
* Removed last bits of implementation details from the API: now uses List<> instead of ArrayList<> (Egon Willighagen <[email protected]>)
* Removed output to STDOUT (Egon Willighagen <[email protected]>)
* Fixed some spelling errors and added JavaDoc links (Egon Willighagen <[email protected]>)
* Synchronized behavior with the MDLV2000Reader (addressing bug #2942196) (Egon Willighagen <[email protected]>)
* Added missing @cdk.bug tag and used interfaces where possible (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* added a method to make cyclopentane to MoleculeFactory (Stefan Kuhn <[email protected]>)
* Added missing unit test for getClosestAtom(double, double, IAtomContainer, IAtom) (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added a unit test to see of the calculated bond length average includes bonds in all IAtomContainer's (Egon Willighagen <[email protected]>)
* Added second test for getClosestAtom(), now with more than two atoms (Egon Willighagen <[email protected]>)
* Added E and Z as allowed configurations (Egon Willighagen <[email protected]>)
* Added UP_OR_DOWN_INVERTED, which is the equivalent of UP_OR_DOWN but with a different stereocenter (Egon Willighagen <[email protected]>)
* Extended JavaDoc, explaining how these IBond.Stereo types define the stereocenter, and indicating for each type explicitly which atom is the stereocenter (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* Added a getBondLengthAverage(IReaction reaction) method, a rewritten version of 1cab8c3c9350ada9b1d054712189720c865e502a by Stefan Kuhn, and the matching unit test (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Ant has a release 1.8 that should be accepted in build.xml (Mark Rynbeek <[email protected]>)
* Master is open for patches... (Egon Willighagen <[email protected]>)
1.3.4
--------
* RGroup queries (Mark Rynbeek <[email protected]>)
* Junit test data for RGroup queries (Mark Rynbeek <[email protected]>)
* R-group query changes for MDL reading/writing (Mark Rynbeek <[email protected]>)
* Fixed taking into account larger ring systems when one ring is in itself already aromatic (fixes #2976054) (Egon Willighagen <[email protected]>)
* Fixed cloning of properties with null values by always using HashMap (fixes #2975800) (Egon Willighagen <[email protected]>)
* Added four and six coordinate neutral platinum atom types. (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added InChI, and link to existing pyrolle test, using a different SMILES (Egon Willighagen <[email protected]>)
* Added tests for two cases of aromatic rings (Stefan Kuhn <[email protected]>)
* Updated the OpenJavaDocCheck library to 0.3 (Egon Willighagen <[email protected]>)
* Added @cdk.bug annotation, and restricted testing to the bug (Egon Willighagen <[email protected]>)
* Removed try/catch to retain the stacktrace of where the NPE occurs (Egon Willighagen <[email protected]>)
* Test checking for NPE when cloning with property with null as value (Arvid Berg <[email protected]>)
* Improved JavaDoc: (Egon Willighagen <[email protected]>)
* Fixed line lengths (Egon Willighagen <[email protected]>)
* Added a test to MDLRXNReaderTest which checks of different numbering for the same mapping gives the same result. x (Stefan Kuhn <[email protected]>)
* The shiftContainer method did not correctly calculate how much the container needs to to shifted. (Stefan Kuhn <[email protected]>)
* 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 <[email protected]>)
* made logging in the AllRingsFinder optional, this helps with performance. (Stefan Kuhn <[email protected]>)
* 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 <[email protected]>)
* Added unit tests for atom type perception of more N.planar3 atom types (Egon Willighagen <[email protected]>)
* Added missing copyright statement and import (Egon Willighagen <[email protected]>)
* The MDLWriter ignored titles when writing a ChemModel (Stefan Kuhn <[email protected]>)
* Simplified the ILoggingTool interface by using Object... (Egon Willighagen <[email protected]>)
* Added IO option to allow saving aromatic SMILES (Egon Willighagen <[email protected]>)
* Added missing unit testing for the SMILESWriter (Egon Willighagen <[email protected]>)
1.3.5
--------
* Fix for getBestAlignmentForLabelXY (Arvid Berg <[email protected]>)
* Test for getBestAlignmentForLabelXY (Arvid Berg <[email protected]>)
* Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality (Rajarshi Guha <[email protected]>)
* fixed PMD errors on Use instanceof against interfaces not implementations and few more Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality (Rajarshi Guha <[email protected]>)
* Introducing PMD test for CDK specific issues: (Egon Willighagen <[email protected]>)
* Removed unstable forcefield code (Egon Willighagen <[email protected]>)
* Added copyright and license header (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* updated test cases Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* add on patches (Syed Asad Rahman <[email protected]>)
* fixed makeAtomsMapOfBondsMap with test (Syed Asad Rahman <[email protected]>)
* Emergency fix: IAminoAcid instead of AminoAcid (Egon Willighagen <[email protected]>)
* A few more interfaces instead of implementations (Egon Willighagen <[email protected]>)
* Replaced use of implementations by interfaces (Egon Willighagen <[email protected]>)
* Use an interface instead of an implementation as type (Egon Willighagen <[email protected]>)
* Use interfaces instead of implementation (Egon Willighagen <[email protected]>)
* MDL reading and writing atom value line, including test cases (M L Rijnbeek <[email protected]>)
* Added another test to check that a query larger than the target does not match (Rajarshi Guha <[email protected]>)
* Test cases for MCS updated (Syed Asad Rahman <[email protected]>)
* updated MCS solution count in the VF lib, depricated turbo MCS and provided methods for timeout (Syed Asad Rahman <[email protected]>)
* updated test for single atom (Syed Asad Rahman <[email protected]>)
* Replaced outdated URL with entry in WikiPedia (fixes #3002741) (Egon Willighagen <[email protected]>)
* Fixed outdated JavaDoc I forgot to remove (fixes #3002409) (Egon Willighagen <[email protected]>)
* Included the qm module in the dist-all (fixes #3002622) (Egon Willighagen <[email protected]>)
* Cleaned up unthrown exceptions (Rajarshi Guha <[email protected]>)
* Removed use of SMARTS parser in the test code so that a new dependency is not required (Rajarshi Guha <[email protected]>)
* removed unwated checks (Syed Asad Rahman <[email protected]>)
* commented unused code (Syed Asad Rahman <[email protected]>)
* test cases for the IQueryAtomContainer support in the SMSD with exceptions fixed (Syed Asad Rahman <[email protected]>)
* test cases for the IQueryAtomContainer support in the SMSD (Syed Asad Rahman <[email protected]>)
* IQuery* support for the SMSD, will help in SMART based searches (Syed Asad Rahman <[email protected]>)
* Turbomode MCS search added (Syed Asad Rahman <[email protected]>)
* Turbo mode MCS search added Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* removed unwanted test case Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* VF Sub search turbo mode (Syed Asad Rahman <[email protected]>)
* Updated the SMSD code for turbo mode substructure search Refactored the SMSD class itself (Syed Asad Rahman <[email protected]>)
* 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 <[email protected]>)
* Added two more unit tests, related to ring closing (Egon Willighagen <[email protected]>)
* SMILES @ and @@ chiralities are now fully read. (Egon Willighagen <[email protected]>)
* Added unit tests with various chiral SMILES situations. (Egon Willighagen <[email protected]>)
* Implemented stereo chemistry for atoms with four ligands (Egon Willighagen <[email protected]>)
* Patch to generalize the stereo chemistry handling. (Egon Willighagen <[email protected]>)
* Minor fix to build.xml to ensure that SMSD code gets included in the large jar file (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* The RXNReaders/Writers now all handle Atom-Atom-Mappings. This was only done in the MDLRXNReader till now (Stefan Kuhn <[email protected]>)
* 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 <[email protected]>)
* Flexibility for ring start angles. (mark_rynbeek <[email protected]>)
* more mdl reader writer tests (Stefan Kuhn <[email protected]>)
* Revert "Additional constant" (Stefan Kuhn <[email protected]>)
* Added a test case for short line mol files. Patch by S.Kuhn, reworked by M.Rijnbeek. (Stefan Kuhn <[email protected]>)
* MDL reading and writing UP_OR_DOWN (Stefan Kuhn <[email protected]>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <[email protected]>)
* Removed the R-based model package and associated jar files and test code (Rajarshi Guha <[email protected]>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <[email protected]>)
* Removed the R-based model package and associated jar files and test code (Rajarshi Guha <[email protected]>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <[email protected]>)
* Removed DocCheck from Eclipse' Build Path (Egon Willighagen <[email protected]>)
* Removed obsolete castings, or replaced by more general ones (Egon Willighagen <[email protected]>)
* added @Test Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* added CDKRMapHandlerTest (Syed Asad Rahman <[email protected]>)
* added CDKRMapHandlerTest Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* The big SMSD patch. (Syed Asad Rahman <[email protected]>)
* Fixed a ClassCastException in a unit test; I messed up (mea culpa) (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors (Egon Willighagen <[email protected]>)
* Added missing cloning of single electrons (Egon Willighagen <[email protected]>)
* Do not try to clone the atom if it does not exist (Egon Willighagen <[email protected]>)
* MDL reading and writing valency (Stefan Kuhn <[email protected]>)
* Line separator fix for RGroup writer (Mark Rijnbeek <[email protected]>)
* de-Javadoc numerous comments (fixes #2980066) (Carl Masak <[email protected]>)
* More extensive testing for removeHydrogens in atomcontainers with hetero atoms without Hs (Stefan Kuhn <[email protected]>)
* Be a bit more forthcoming with debug messages: report also the parameter types of the method (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* converted uses of indexOf to startsWith/contains (Rajarshi Guha <[email protected]>)
* Updated HIN reader to fix bug 2984581 (Rajarshi Guha <[email protected]>)
* Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten (Egon Willighagen <[email protected]>)
* Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original (Egon Willighagen <[email protected]>)
* Removed duplication of cloning. (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too (Egon Willighagen <[email protected]>)
* Fixed a typo in the test method name (Egon Willighagen <[email protected]>)
* Got rid of some debug prints (Rajarshi Guha <[email protected]>)
* Fixed a regex bug which prevented the engine from properly loading descriptor class names (Rajarshi Guha <[email protected]>)
* Some code cleanup to make it more idiomatic Java (Rajarshi Guha <[email protected]>)
* New IChemObjectBuilder interface: (Egon Willighagen <[email protected]>)
* Bumped version to indicate this is post 1.3.4 release (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
1.3.6
--------
* Updated copyright to 2010 (Egon Willighagen <[email protected]>)
* Compare values not objects (fixes #3061263) (Egon Willighagen <[email protected]>)
* Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object (Egon Willighagen <[email protected]>)
* Smiles parser setting to preserve aromaticity as provided in the Smiles String itself. (Mark Rynbeek <[email protected]>)
* 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 <[email protected]>)
* Renabled test which was (accidentally?) outcommented when switching to JUnit4 in commit 06a1a3dd (Egon Willighagen <[email protected]>)
* Added a reference to the original Wiener paper (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Minor cleanup: corrected copyright statement; simplified JavaDoc by removing empty parameter table (Egon Willighagen <[email protected]>)
* Replaced inline citation by reference to the main bibliography (Egon Willighagen <[email protected]>)
* Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms (Rajarshi Guha <[email protected]>)
* Updated javadocs and added extra unit test (Rajarshi Guha <[email protected]>)
* Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms (Rajarshi Guha <[email protected]>)
* Removed output to STDOUT (Egon Willighagen <[email protected]>)
* Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br (Saravanaraj <[email protected]>)
* Unit test for bug #3040273. (Saravanaraj <[email protected]>)
* Fixed hybridization information: these are sp3 hybridized systems (Egon Willighagen <[email protected]>)
* More missing elements for SMILES parsing problems reported in bug #3048501 (Egon Willighagen <[email protected]>)
* Unit tests for SMILES parsing bugs reported in #3048501 (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* JavaDoc fixes: correct @cdk.cite use, and small typo (Egon Willighagen <[email protected]>)
* Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890) (Egon Willighagen <[email protected]>)
* Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) (Egon Willighagen <[email protected]>)
* Added the maven build file (closes #3042475) (Egon Willighagen <[email protected]>)
* a)removed blank/unused methods and fixed imports Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* a)IMatch to Match and constructor call for state used TargetProperties for faster processing Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* a)Assert cleaned and fixed b)Correct ASSERT imports used (Syed Asad Rahman <[email protected]>)
* Removed unused code (Syed Asad Rahman <[email protected]>)
* Updated checking of indices which now are -1 if unset, instead of null (Syed Asad Rahman <[email protected]>)
* 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 <[email protected]> (Syed Asad Rahman <[email protected]>)
* a)Refactored matchers, atom matcher and bond matcher b)getTanimoto score fixed for single atoms (Syed Asad Rahman <[email protected]>)
* Updates for the getImplicitHydrogenCount() renaming (Egon Willighagen <[email protected]>)
* The smsd module now depends on the signature module (Egon Willighagen <[email protected]>)
* Latest SMSD code 1.2.0: Major changes are: (Syed Asad Rahman <[email protected]>)
* Use the factory to not depend on an implementation (Egon Willighagen <[email protected]>)
* Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per report #3020065 (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Also take into account super classes (Egon Willighagen <[email protected]>)
* Renamed MDLWriter into MDLV2000Writer (implements #3029447) (Egon Willighagen <[email protected]>)
* Assert pattern has the expected value as first argument (Egon Willighagen <[email protected]>)
* Use the builder pattern to instantiate an IIsotope (Egon Willighagen <[email protected]>)
* MDLV2000 reader interprets D and T without M ISO line mandatory (Mark Rynbeek <[email protected]>)
* Use the PT class to see if something can be an element and removing the redundant element symbol info (Egon Willighagen <[email protected]>)
* Fixed annotation with TestMethod, not TestClass (fixes #3016632) (Egon Willighagen <[email protected]>)
* Skip inner classes for @cdk.module and @cdk.githash JavaDoc tests (fixes #3043084) (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* Assert the compound is aromatic (fixes false negative) (Egon Willighagen <[email protected]>)
* Exporting the signatures jar (maclean <[email protected]>)
* Removed the OpenJavaDocCheck Jazzy extension which was not supposed to go in; it's not ready for prime time (Egon Willighagen <[email protected]>)
* Added missing dependencies (fixes failing unit tests) (Egon Willighagen <[email protected]>)
* Added missing dependencies (fixes failing unit tests) (Egon Willighagen <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* Release CDK 1.2.6.1 (Egon Willighagen <[email protected]>)
* Copy the 2D templates into the source distribution (Egon Willighagen <[email protected]>)
* Added finally blocks to MolHandler to close its input streams, with proper logging calls if it fails Fixes bug #3032568 (Jules Kerssemakers <[email protected]>)
* UIT timeout fix (Andreas Truszkowski <[email protected]>)
* Cleaned up exception handling in TemplateHandler.loadTemplates() to be more specific and less pessimistic. (Jules Kerssemakers <[email protected]>)
* QSAR descriptor values made serializeable (Andreas Truszkowski <[email protected]>)
* Fixed assertion to compare two Vector3d's (Egon Willighagen <[email protected]>)
* Added test to assert that two Vector3d's are identical (Egon Willighagen <[email protected]>)
* All methods now tested (maclean <[email protected]>)
* Hooking up test machinery (maclean <[email protected]>)
* Altered the getTetrahedralDescription to be get stereo and return ITetrahedralChirality.Stereo (maclean <[email protected]>)
* Moved Stereotool to stereo package (maclean <[email protected]>)
* Convenience method that returns chirality descriptor (R/S) given four atoms in priority order (maclean <[email protected]>)
* Missing docs (maclean <[email protected]>)
* Copyright statements (maclean <[email protected]>)
* Just to be paranoid, test +/- tetrahedra above and below the XY plane (maclean <[email protected]>)
* Tests for square planar shapes, trig bipyr, and oct (maclean <[email protected]>)
* Cleanup and fixing (I think) of the trigonal bipyramidal method (maclean <[email protected]>)
* Test for 3 colinear points (maclean <[email protected]>)
* Better docs (maclean <[email protected]>)
* Tests for tetrahedral sign, some basic defined vectors (maclean <[email protected]>)
* Test class, and name change of distanceToPlane to show that it returns signed (+/-) distance (maclean <[email protected]>)
* Initial go at the StereoTool - functions taken from Jmol's smiles package for 3D stereo checking (maclean <[email protected]>)
* Updated OB note and robustified unit tests (Rajarshi Guha <[email protected]>)
* Added support for multi-molecule mol2 files. Updated source and added unit test and test file (Rajarshi Guha <[email protected]>)
* Updated cdk-1.2.x patches for master API (Egon Willighagen <[email protected]>)
* Release 1.2.6 (Egon Willighagen <[email protected]>)
* Updated the DebugBond unit test too now: new DebugBond() has zero atoms (Egon Willighagen <[email protected]>)
* Backport patch, to make the patches compile with cdk-1.2.x (Egon Willighagen <[email protected]>)
* Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. (Egon Willighagen <[email protected]>)
* Also fix the new NNBond() == 0 atoms for the nonotify module (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Updated test to assume new Bond() creates a bond with zero atoms (Egon Willighagen <[email protected]>)
* Added two unit tests for aromatic N-oxides that are the basis for failures in SMARTS matching (Rajarshi Guha <[email protected]>)
* added javadoc to IChemObjectReader explaining the split between ISimple and IIterating ChemObjectReaders (Jules Kerssemakers <[email protected]>)
* Exceptions when clone atomless ISingleElectron and ILonePair too (Egon Willighagen <[email protected]>)
* Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms (Egon Willighagen <[email protected]>)
* Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010 (Egon Willighagen <[email protected]>)
* Added the N.oxide atom type, for structures like (CH3)N=O (Egon Willighagen <[email protected]>)
* Fixed reading of SD properties: keep the first line too (Egon Willighagen <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* Fixed unit test: surely there is no atom with symbol 0... how long has this been failing?? (Egon Willighagen <[email protected]>)
* Updated fingerprinter javadoc (Rajarshi Guha <[email protected]>)
* Added a test class to aromaticity of three compounds: the last incorrectly fails (Egon Willighagen <[email protected]>)
* Also except N.amide as part of an aromatic ring (Egon Willighagen <[email protected]>)
* Added a test class to repeat atom type perception and test consistency (Egon Willighagen <[email protected]>)
* Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up (Egon Willighagen <[email protected]>)
* Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then (Egon Willighagen <[email protected]>)
* BooleanIOSetting to let MDLWriter output bond type 4 (aromatic) (Mark Rijnbeek <[email protected]>)
* Reorderd imports (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* chemfilter improvised Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* added ExtAtomContainerManipulator Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* deleted ext Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* updated SMSD code Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* updated SMSD code Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* Convenience constructors for AtomSignature that take IAtoms rather than atom indices (maclean <[email protected]>)
* Added missing jar meta file for the Signatures library (Egon Willighagen <[email protected]>)
* Updated to reflect the upstream jar name (Egon Willighagen <[email protected]>)
* Abstract methods not part of API are now protected, to discourage thier use (maclean <[email protected]>)
* Various fixes to tests (maclean <[email protected]>)
* Added the missing assert: runCoverageTest() returns a boolean stating the success (Egon Willighagen <[email protected]>)
* cdk.cite references for two Faulon papers (maclean <[email protected]>)
* More missing javadocs - notably the class documentation for AtomSignature and MoleculeSignature (maclean <[email protected]>)
* Mising constructor javadoc, and inheritdoc annotation on AtomSignature (maclean <[email protected]>)
* Final missing test (maclean <[email protected]>)
* Atom signature test methods (maclean <[email protected]>)
* Molecule signature tests (maclean <[email protected]>)
* Signature quotient graph test method (maclean <[email protected]>)
* Missing test for Orbit::iterator (maclean <[email protected]>)
* Removed unused import (Egon Willighagen <[email protected]>)
* Molecule From Signature Builder tests (maclean <[email protected]>)
* All orbit methods tested (maclean <[email protected]>)
* Finally correct junit annotations, and sort test (maclean <[email protected]>)
* BeforeClass method must be static; better clone test (maclean <[email protected]>)
* Fixes some problems flagged by PMD (maclean <[email protected]>)
* Use junit's BeforeClass instead of Before annotation (maclean <[email protected]>)
* Added missing githash tags, to add links in the JavaDoc to the source code repository (Egon Willighagen <[email protected]>)
* Inherit JavaDoc where methods overwrite a super method (Egon Willighagen <[email protected]>)
* Fixed PMD warnings: more descriptive field names; use of Integer.valueOf() (Egon Willighagen <[email protected]>)
* Added test method annotation for the clone() method (Egon Willighagen <[email protected]>)
* Removed some unnecessary imports (maclean <[email protected]>)
* Test orbit cloning (maclean <[email protected]>)
* Improved canonical label method in graph signature (maclean <[email protected]>)
* Integer invariants, and updated signatures jarfile (maclean <[email protected]>)
* Added JavaDoc HTML generation for the signature module (Egon Willighagen <[email protected]>)
* Hooked in PMD testing for the signature module (Egon Willighagen <[email protected]>)
* Defined dependencies for the test module (Egon Willighagen <[email protected]>)
* Hooked the signature module into the CDK build system (Egon Willighagen <[email protected]>)
* Removed the dependency on the nonotify module (Egon Willighagen <[email protected]>)
* Created a CDK style module test suite (Egon Willighagen <[email protected]>)
* MoleculeFromSignatureBuilder tests (maclean <[email protected]>)
* Extend from CDKTestCase and use the slow running test check (maclean <[email protected]>)
* Fixed and cleaned up molecule signature tests (maclean <[email protected]>)
* Initial commit of signature package (maclean <[email protected]>)
* Added OpenJavaDocCheck 0.5 - the Jazzy spell checking extension (Egon Willighagen <[email protected]>)
* specify fail behavior (returns null) in javadoc (jonalv <[email protected]>)
* Added PMD tests for detecting misuse of TestClass and TestMethod, e.g. TestClass on a method. (fixes #3014808) (Egon Willighagen <[email protected]>)
* Removed two lines added in master to the removed doccheck target (Egon Willighagen <[email protected]>)
* Improved javadoc generation using a link tag, so that references to java library classes are resolved properly (maclean <[email protected]>)
* Update OpenJavaDocCheck to 0.5: fixing a few false positives (Egon Willighagen <[email protected]>)
* Removed use of the proprietary DocCheck utility (Egon Willighagen <[email protected]>)
* OpenJavaDocCheck errors are fixed for SMSD related modules Signed-off-by: Syed Asad Rahman <[email protected]> (Syed Asad Rahman <[email protected]>)
* solved cdk-Bugs-3006773 : small JavaDoc errors in the smsd module (Syed Asad Rahman <[email protected]>)
* Fix for character spacing for "APO" line in RGFile output (Mark Rynbeek <[email protected]>)
* Branch open for commits for the future 1.3.6 (Egon Willighagen <[email protected]>)
* Use the new tests in more situations (Egon Willighagen <[email protected]>)
1.3.7
--------
* Replaced the broken links with new ones (fixes #3108471) (Egon Willighagen <[email protected]>)
* Upgraded to the final JNI-InChI 0.7: (Egon Willighagen <[email protected]>)
* Renamed test class to conform the expected naming pattern (Egon Willighagen <[email protected]>)
* Factored out a AbstractCDKObjectTest now used in AbstractAtomParity test, to add the missing unit test (Egon Willighagen <[email protected]>)
* Overwrite the default public constructor because this class is not supposed to be instantiated. (Egon Willighagen <[email protected]>)
* Added missing TestMethod annotation (Egon Willighagen <[email protected]>)
* Added missing unit test (Egon Willighagen <[email protected]>)
* Strongly typed the comparator, removing no longer valid tests (Egon Willighagen <[email protected]>)
* Removed an obsolete test (Egon Willighagen <[email protected]>)
* Fixed unit test: test the correct class (Egon Willighagen <[email protected]>)
* Added missing TestMethod annotation (Egon Willighagen <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* Renamed methods according to naming coverage testing naming scheme (Egon Willighagen <[email protected]>)
* Added missing classificatins to some descriptors (Rajarshi Guha <[email protected]>)
* Use a builder more efficiently (Egon Willighagen <[email protected]>)
* Added missing sulphur atom type as found in thiosulphonate (fixes #3080848) (Egon Willighagen <[email protected]>)
* Added acidic and basic group count descriptors (implements #3056330) (Egon Willighagen <[email protected]>)
* Added missing atom type: positively charged P with three neighbors, of which one double bonded (Egon Willighagen <[email protected]>)
* Added a unit test for the C=[N+]=[N-] functional group (Egon Willighagen <[email protected]>)
* Updated string generation for molecular formulae that address bug 3071473 (Rajarshi Guha <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* Added unit test for bug 2871303, which appears to be resolved now (Rajarshi Guha <[email protected]>)
* Added unit test for bug 2853035, which appears to be resolved now (Rajarshi Guha <[email protected]>)
* Added unit test for bug 3001616, which appears to be resolved now (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Removed merge artefact (Egon Willighagen <[email protected]>)
* test for streams returning false on ready() (vedina <[email protected]>)
* Revert "Updated isotope to have proper equals and hashCode methods" (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* Updated Javadocs, since Egon is a nice guy :) (Rajarshi Guha <[email protected]>)
* Actually put in a test (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* Updated isotope to have proper equals and hashCode methods (Rajarshi Guha <[email protected]>)
* Added unit test and test file for bug 2917084 (Rajarshi Guha <[email protected]>)
* Added coverage testing for constructors (Egon Willighagen <[email protected]>)
* Fixed the CDKSourceCodeWrite to create compilable source code (Egon Willighagen <[email protected]>)
* Added use of Groovy to test if the output compiles (Egon Willighagen <[email protected]>)
* Updated Murcko code so that we save the appropriatley cloned framework. Also updated unit tests (Rajarshi Guha <[email protected]>)
* Added missing entry for compiling the iordf module (Egon Willighagen <[email protected]>)
* Updated for API changes in the IChemObjectBuilder (Egon Willighagen <[email protected]>)
* Updated for API change for get/setImplicitHydrogens() (Egon Willighagen <[email protected]>)
* Copied the inchi module into the sinchi module, providing Standard InChI support with JNI-InChI 0.7. (Egon Willighagen <[email protected]>)
* Added iordf to the ojdcheck target (Egon Willighagen <[email protected]>)
* Added missing dependencies for the test module for iordf (Egon Willighagen <[email protected]>)
* Added missing JavaDoc for the iordf module (Egon Willighagen <[email protected]>)
* Added missing JavaDoc (Egon Willighagen <[email protected]>)
* Fixed a PMD warning: too short variable name (Egon Willighagen <[email protected]>)
* Reduced complexity by introducing two maps (Egon Willighagen <[email protected]>)
* Prefixed the hybridization constants with HYBRID_ (Egon Willighagen <[email protected]>)
* Made final static full upper case, as requested by PMD (Egon Willighagen <[email protected]>)
* Removed output to STDOUT (Egon Willighagen <[email protected]>)
* Added iordf to dist-large (Egon Willighagen <[email protected]>)
* Added (de)serialization of the IPseudoAtom fields to RDF (Egon Willighagen <[email protected]>)
* Added (de)serialization of the IElectronContainer fields to RDF (Egon Willighagen <[email protected]>)
* Added (de)serialization of the IIsotope fields to RDF (Egon Willighagen <[email protected]>)
* Added a few missing dependencies (Egon Willighagen <[email protected]>)
* Fixed module allocation (Egon Willighagen <[email protected]>)
* Added roundtripping for IAtomType.formalCharge (Egon Willighagen <[email protected]>)
* Hooked in testing for iordf (Egon Willighagen <[email protected]>)
* Reuse of earlier extracted helper methods (Egon Willighagen <[email protected]>)
* Added roundtripping of IAtom.atomtypeName and .maxBondOrder (Egon Willighagen <[email protected]>)
* Test all bond types (Egon Willighagen <[email protected]>)
* Added roundtrip of IElement.atomicNumber and IAtomType.hybridization (Egon Willighagen <[email protected]>)
* Added roundtrip of IChemObject.identifier (Egon Willighagen <[email protected]>)
* Added read and write of IBond and .order (Egon Willighagen <[email protected]>)
* Added class JavaDoc (Egon Willighagen <[email protected]>)
* Added method to create identifiers based on the hashCode (Egon Willighagen <[email protected]>)
* Added read/write of IAtom.symbol in RDF (Egon Willighagen <[email protected]>)
* Added a Java API version of the CDK ontology (not synched to the OWL) (Egon Willighagen <[email protected]>)
* Added reader and writer for the CDKOWL/N3 format (Egon Willighagen <[email protected]>)
* Added framework to convert the CDK data model into a JEna Model (Egon Willighagen <[email protected]>)
* Defined a new format, serializing the CDK data model into the Web Ontology Language (OWL) in the Notation3 (N3) format. (Egon Willighagen <[email protected]>)
* Bumped version to indicate it is the development version (Egon Willighagen <[email protected]>)
* Throw a change event when an existing property is removed (fixes #2993561). (Egon Willighagen <[email protected]>)
* Do no pass stereo information when none (null) was read (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added testing of the isOK() method (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added a constructor to set a custom ring finder instance (e.g. with a time out set) (Egon Willighagen <[email protected]>)
* Added build/*.javafiles to the .classpath so that the coverage unit tests succeed in Eclipse (Egon Willighagen <[email protected]>)
* modified to avoid InputStreamReader.ready() method (vedina <[email protected]>)
* Added unit tests for bug 3088164 (Rajarshi Guha <[email protected]>)
* Updated to ensure that we properly handle tag separator lines that may not be completely empty (Rajarshi Guha <[email protected]>)
* Fixed bug in reading a SDF property whose value is a single space (Rajarshi Guha <[email protected]>)
* removed debug code and add another check in the unit test (Rajarshi Guha <[email protected]>)
* Added another unit test (Rajarshi Guha <[email protected]>)
* 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 <[email protected]>)
* Added new test method for aromatic bonds (Egon Willighagen <[email protected]>)
* Build molecules with aromatic bonds if labelled with 'p' (maclean <[email protected]>)
* Aromatic bond (output) support for signatures (maclean <[email protected]>)
* - 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 <[email protected]>)
* Added a format definition for the output of the MoSS software (Egon Willighagen <[email protected]>)
* Check for a null major isotope, which happens with R-groups (maclean <[email protected]>)
* Small typo fix to point to the correct test class (Egon Willighagen <[email protected]>)
* Four unit tests that test if the fingerprint calculation is affected by atom or bond permutation (Egon Willighagen <[email protected]>)
* Updated version and confirmed inception year (Egon Willighagen <[email protected]>)
* Updated getVersion method to not print to stdout (Rajarshi Guha <[email protected]>)
1.3.8
--------
* Updated the changelog (Egon Willighagen <[email protected]>)
* Updated the README (Egon Willighagen <[email protected]>)
* Bumped version for release 1.3.8 (Egon Willighagen <[email protected]>)
* Added description of IO settings to the writers JavaDoc (fixes #3029445) (Egon Willighagen <[email protected]>)
* Added missing unit tests (Egon Willighagen <[email protected]>)
* Changed method names to versions expected by the coverage testing system (Egon Willighagen <[email protected]>)
* Added missing test annotation (Egon Willighagen <[email protected]>)
* Added missing dependency (Egon Willighagen <[email protected]>)
* Fixed returning the monomer names when no strands are defined (Egon Willighagen <[email protected]>)
* Fixed counting the number of monomers when no strands are defined (Egon Willighagen <[email protected]>)
* Restored the previous behavior of a zero default charge, fixing very many unit tests (Egon Willighagen <[email protected]>)
* Moved packaging of the PeriodicTable data to the new model too (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Moved the test classes from the standard to the core TestSuite too (Egon Willighagen <[email protected]>)
* Updated module assignments (Rajarshi Guha <[email protected]>)
* Added unit tests for H-bond donor/acceptor for bug #3133610 (Egon Willighagen <[email protected]>)
* Fixed typo in JavaDoc (Egon Willighagen <[email protected]>)
* Fixed isotope class to get the proper isotope if mass number is available, rather than using the major isotope by default (Rajarshi Guha <[email protected]>)
* Added some documentation for possibly non-obvious methods (Rajarshi Guha <[email protected]>)
* AminoAcidCountDescriptor constructor made thread safe (Andreas Truszkowski <[email protected]>)
* System.out.println() removed in ProtonTotalPartialChargeDescriptor.java (Andreas Truszkowski <[email protected]>)
* Added missing copyright/license and cdk.module statements (Egon Willighagen <[email protected]>)
* Added missing JavaDoc and unit tests for VisitedAtoms (Egon Willighagen <[email protected]>)
* Added a simple code example for how to use the CIPTool (Egon Willighagen <[email protected]>)
* Made a few classes private to the package (Egon Willighagen <[email protected]>)
* Added comment in JavaDoc about the sorted nature of the method input (Egon Willighagen <[email protected]>)
* Added unit test for aromatic molecular signatures (Egon Willighagen <[email protected]>)
* Added testing of bromochlorofluoroiodomethane (Egon Willighagen <[email protected]>)
* Only consider recursion if all ligand atoms are identical and equal in number (fixes R detection in PubChem CID 42475007) (Egon Willighagen <[email protected]>)
* Keep track of which atoms have already been visited, to properly terminate when we give up (Egon Willighagen <[email protected]>)
* Added unit tests to uncover a non-termination issue in the CIP algorithm reported by Ola (Egon Willighagen <[email protected]>)
* Added unit test to make sure no chirality is detected for the FC(Me)(Me)R carbon (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Test case provided by Gilleain around termination, using the SMILES as input (Egon Willighagen <[email protected]>)
* Set up a CIP module. (Egon Willighagen <[email protected]>)
* Added missing @TestMethod annotation for LoggingTool (Egon Willighagen <[email protected]>)
* Added missing @TestMethod annotation (Egon Willighagen <[email protected]>)
* Converted all readers to the new read() API (Egon Willighagen <[email protected]>)
* Branch open for 1.3.8 patches (Egon Willighagen <[email protected]>)
* Compile fixes caused by rebasing artefacts as some modules still change bits in order modules (Egon Willighagen <[email protected]>)
* Refactored reaction boxes into a IGeneratorParameter (Egon Willighagen <[email protected]>)
* Refactored foreground color into a IGeneratorParameter (Egon Willighagen <[email protected]>)
* Refactored showIm/ExplicitHydrogens as IGeneratorParameter (Egon Willighagen <[email protected]>)
* Using IRenderer<T> interface instead of implementation (maclean <[email protected]>)
* More types in renderers, and associations between renderers (maclean <[email protected]>)
* Point to the interfaces rather than the implementation (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Yeah, the last fix. The 'render' module is now PMD, JUnit4, and JavaDoc clean (Egon Willighagen <[email protected]>)
* More JavaDoc and PMD fixes: removed an unused parameter, throws non-generic exception, fixed JavaDoc errors and added missing JavaDoc (render). (Egon Willighagen <[email protected]>)
* Fixed some PMD warnings: longer variable names (render). (Egon Willighagen <[email protected]>)
* Fixed a NPE: if the atom does not have a atomic number defined, return the default color (Egon Willighagen <[email protected]>)
* Added missing unit tests and matching annotation for the render module (Egon Willighagen <[email protected]>)
* Added a few missing test methods for the RendererModel (Egon Willighagen <[email protected]>)
* Added missing TestClass/-Method annotations and test methods for the default colors (Egon Willighagen <[email protected]>)
* JavaDoc updates: added missing bits (render). (Egon Willighagen <[email protected]>)
* Added missing dependency of test-render on annotation (Egon Willighagen <[email protected]>)
* Report the unregistered parameter class name (Egon Willighagen <[email protected]>)
* 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 <[email protected]>)
* Added the RendererModel.get(paramType) convenience method (Egon Willighagen <[email protected]>)
* Renamed get/setRenderingParameter methods to shorter names (render). (Egon Willighagen <[email protected]>)
* Throw an exception when a parameter value is requested, but not set yet by registering the appropriate generator (Egon Willighagen <[email protected]>)
* Added getDefaultRenderingParameter convience method, using generics powers (Egon Willighagen <[email protected]>)
* Added setRenderingParameter convenience method, using generics powers (Arvid Berg <[email protected]>)
* Removed obsolete RenderingPatameters class (Egon Willighagen <[email protected]>)
* Changed wedge width to rendering parameter (maclean <[email protected]>)
* Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (render). (Egon Willighagen <[email protected]>)
* Moved ExternalHighlightColor into RendererModel for now, to solve a compile dependency (Egon Willighagen <[email protected]>)
* Converted hoverOverColor to the new rendering parameter API (Egon Willighagen <[email protected]>)
* Converted externalHighlightColor to the new rendering parameter API (Egon Willighagen <[email protected]>)
* Converted mappingColor and mappingLineWidth to the new rendering parameter API (Egon Willighagen <[email protected]>)
* Converted boundsColor to the new rendering parameter API (Egon Willighagen <[email protected]>)
* Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API (Egon Willighagen <[email protected]>)
* Fixed returning of the actual paramater value, instead of a new instance all the time: getClass().getClass() != getClass() (Egon Willighagen <[email protected]>)
* Unit test for returning the parameter value, instead of a new instance all the time (Egon Willighagen <[email protected]>)
* Removed to unused imports (Egon Willighagen <[email protected]>)
* Split up the old IGenerator interface into IGenerator and IAtomContainerGenerator, the first now only containing the method for getting the parameters (Egon Willighagen <[email protected]>)
* Factored out a ColorHash IRenderingParamater (Egon Willighagen <[email protected]>)
* Converted BondDistance into an IGeneratorParameter (Egon Willighagen <[email protected]>)
* Converted FontName and FontStyle into IGeneratorParameters (Egon Willighagen <[email protected]>)
* Converted useAntiAliasing into a IGeneratorParameter (Egon Willighagen <[email protected]>)
* Converted ringProportion to IGeneratorParameter variants (Egon Willighagen <[email protected]>)
* Converted showAromaticity and cdkStyleAromaticity to IGeneratorParameter variants (Egon Willighagen <[email protected]>)
* Converted bondWidth and defaultBondColor into IGeneratorParameter's (Egon Willighagen <[email protected]>)
* Removed last four rendering parameters from BasicAtomGenerator: isCompact, compactShape, isKekule, and showEndCarbons (Egon Willighagen <[email protected]>)
* Moved the atom radius into the new rendering parameter API (renderbasic module) (Egon Willighagen <[email protected]>)
* Moved rendering parameters for atom draw colors to the new IGeneratorParameter API (Egon Willighagen <[email protected]>)
* Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator (Egon Willighagen <[email protected]>)
* Added a method to list all rendering parameters know to the current renderer (Egon Willighagen <[email protected]>)
* Added missing @cdk.githash tags (Egon Willighagen <[email protected]>)
* The default atom color is white, not black, according to the implementation (Egon Willighagen <[email protected]>)
* Fixed a null pointer exception: return the default color, if the atom has no charge (Egon Willighagen <[email protected]>)
* Updated test: apparently, the values for Color.PINK can change between JVM releases? (Egon Willighagen <[email protected]>)
* Made method public static, as expected by the JUnit framework (Egon Willighagen <[email protected]>)
* Converted margin into the RenderingParameter variant (Egon Willighagen <[email protected]>)
* Changed generic definition (Arvid Berg <[email protected]>)
* Moved the atom radius into the new rendering parameter API (render module) (Egon Willighagen <[email protected]>)
* Moved rendering parameters for atom draw colors to the new IGeneratorParameter API (Egon Willighagen <[email protected]>)
* Set up a API to retrieve a IRenderingParameter from the RenderModel (Egon Willighagen <[email protected]>)
* Return the default if the value has not been overwritten with setValue() (Scooter Morris <[email protected]>)
* Changed getParameters() to use IGeneratorParameter<?> (Arvid Berg <[email protected]>)
* 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 <[email protected]>)
* 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 <[email protected]>)
* Added missing JavaDoc to render interfaces (Egon Willighagen <[email protected]>)
* Added missing JavaDoc for getColor() methods (Egon Willighagen <[email protected]>)
* Added IRenderer methods needed for the Controllers. (Egon Willighagen <[email protected]>)
* Introducing IRenderer, to solve some dependencies (Egon Willighagen <[email protected]>)
* Setting up the new render infrastructure. (Egon Willighagen <[email protected]>)