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Preparing for the first release in the 1.3 development series
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| version=1.2.3 | ||
| version=1.3.0 |
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| CHANGELOG | ||
| --------- | ||
| This changelog is automatically generated from the: | ||
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| git log --pretty=format:"* %s (%aN <%ae>)" --no-merges <LAST-TAG>..HEAD >> changelog.txt | ||
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| 1.3.0 | ||
| ----------- | ||
| * Removed old changelog files (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Capability to read and write reaction properties information. Added theirs corresponding tests (Miguel Rojas Cherto <miguelrojasch@yahoo.es>) | ||
| * Fixed serialization of IAtom's with null formal charge to not cause NullPointerExceptions (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for serialization of null formal charges into the MDL molfile format (which currently fails) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed a typo from the previous merge (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated Javadocs for SMARTS query tool to indicate unsupported features (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Cleaned up source file to remove spurious line endings (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Bumped version number (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * The formal charge of the IAtomcontainer is transfered to IMolecularFormula (Miguel Rojas Cherto <miguelrojasch@yahoo.es>) | ||
| * Fixed bug 2787332 The old bond array in the gasteiger charge calculation was set to the wrong size (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated to fix bug 2788357 SMARTSQueryTool now catches TokenMgrError in the constructor and throws a CDKException. Also added unit test to check for this (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added new taglet to process cdk.githash tag and link Javadocs to sources in Git repo (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated cdk.svnrev tags to cdk.githash tags (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Bug_2787332. Added test for the Triclosan molecule (InChI=1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,1 6H) the IPMolecularLearningDescriptor caluclation fails with java.lang.ArrayIndexOutOfBoundsException: 24. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>) | ||
| * Removed obsolete renderer code: either use cdk-1.0.x or jchempaint-primary (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added test for bug 2786624 in the parser test suite (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added links to PMD pages (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added link to JUnit stats (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed links. Suboptimal, as the path is still hardcoded to a single Nightly instance, but we do not have the XML framework yet to summarize things over all Nightlies (running different JDKs, OSs, etc) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Updated version number (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added test to ensure IAtomContainers are not sneaked in via IMoleculeSet.add(IAtomContainerSet) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Overwritten addAtomContainer(IAtomContainer, double) too, to throw an IllegalArgumentException when a non-IMolecule is passed (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Now throws an IllegalArgumentException when it is tried to store an IAtomContainer which is not an IMolecule (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for #2784182 (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * new test with reserpine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>) | ||
| * Added taglets for threading safety (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * With one atom or less, we define it to be connected, as there is no partitioning needed (fixes #2784209, NullPointerException on IAtomContainer with no atoms) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for bug #2784209 which currently fails (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * More removal of explicit org.openscience.cdk package names: throws clauses (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * More removal of explicit org.openscience.cdk package names (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * More removal of explicit org.openscience.cdk package names: for new org.openscience.cdk.Foo() calls (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Removed explicit org.openscience.cdk.interfaces packages names (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Removed explicit package names, in favor of imports, for org.openscience.cdk in the datadebug module (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Removed explicit package names, in favor of imports, for org.openscience.cdk in the data module (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * breakout of recursion option on AllRingsFinder (mark_rynbeek <markr@ebi.ac.uk>) | ||
| * Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>) | ||
| * Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>) | ||
| * Controller of the mass when it is out of the range (Miguel Rojas Cherto <miguelrojasch@yahoo.es>) | ||
| * Updated source and test to address review issues. Updated typos in Javadocs and added link to AllRingFinder. Move instatiation of SMARTS matcher to constructor. The element count array is now of length 120. Updated JUnit test to remove superflous prints and updated copyright (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Moved the pubchem fingerprinter to the fingerprinter module, since it needs SMARTS which is not a dependency of the standard module (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added more test cases comparing our FP's with those provided by Pubchem (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated Javadocs, cleaned up some tests (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added test for benzene (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated SMARTS patterns to use H count specifications rather than explicit H matches (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Initial version of Pubchem fingerprints based on the public domain NCGC code. Includes unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated to intelligently add H's to a PLANAR3 N, fixes bug 2781199 (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added test case for bug 2781199 (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Updated unit tests to employ equals tests. Fixed Javadocs. Address comments wrt the original patch (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * removed needless white space (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Refactored to provide a query container specifically for pharmacophore queries. (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated the toString tests (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added test methods for the new toString methods. Also added test method annotations (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * provided toString methods for the pcore query classes (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added a unit test to ensure SD fields are read for all molecules (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for bug 1579235, which checks for aromaticity in indolizine (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated code to use 1.5 idioms and remove use of Iterator (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added links to PMD pages (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added link to JUnit stats (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Updated build system to take into account non public classes as well. Also updated ChiIndexUtils to be package private (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * split up test (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>) | ||
| * new files (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>) | ||
| * more tests for cml reading (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>) | ||
| * Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed cast, remove redundant full package name (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for #2692107 (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed typo: missing 's' (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed cast, remove redundant full package name (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added unit test for #2692107 (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed typo: missing 's' (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Use the proper folder name, including the CDK version (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * 1.2.1 release being prepared (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed bug 2714283, which properly throws an exception when rings are not closed properly. If a ring is not closed with the appropriate ring number, InvalidSmilesException is thrown. Matches Daylight behavior (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Fixed bug 2729120 and added unit test (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Updated comment to fix bug 2768643. (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Partial fix for bug 2719237. Made getBondOrderSum static, added unit test for it (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Typo: proteinl -> protein (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Made class public, to unbreak adding it to the build/*.javafiles (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Partially fixed SMARTS matching for R0. Updated target molecule initialization to explicitly (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Fixed dubious equality test. A private method was checking Double objects via reference. (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added test method annotation. Completes coverage for data module (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Refactored ChiIndexUtils to make it package private. Cleans up public API, since it is only used by chi descriptor code. Updated all dependent classes. Moved test code (which needs to be filled in!) as well (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Code cleanup of ChiIndexUtils. Converted to 1.5 idioms (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Clean up of PathTools and added test method annotation, so that core is completely covered (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Fixed the previous commit to edit the cdk.keyword line, not the cdk.module line (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * More consistent keywords used (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added a test to ensure that Integer objects are compared by value rather than reference (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added a test case to check that atom container diffs are correct when using deserialized objects (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Fixed IntegerDifference so that it actually checks the integer value rather than references of the Integer object. Fixes the problem whereby an object serialized to disk and then deserialized does not match the original object (i.e., non empty diff string) (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics, one last time... Leander should work by now... (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Use interface instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Some other code cleanup (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics, here too (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics, here too (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Use interface instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added generics (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Removed an unused import (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Use IAtomContainer instead of IMolecule, as the actual matching is using IAtomContainers already (fixes #2686249) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed a ClassCastException (fixes #2685134) (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Added source attrib to fix building the Ubuntu .deb (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed Help build system: use doclet jars in develjar/; updated for new src folder src/main; removed very outdated use of rt.jar (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Removed libdepends include for test-ioformats, which does not actually have libdepends (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Updated so that if a target atom has no symbol (such as pseudo atoms) the match returns false (rather than an NPE) (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Fixed proper handling of #n SMARTS querys (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added test case for bug 2686473 (Rajarshi Guha <rajarshi.guha@gmail.com>) | ||
| * Added note on Ant 1.7.1 required (Egon Willighagen <egonw@users.sourceforge.net>) | ||
| * Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Added a missing dep (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Correction of the solution (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * added method to calculate the Total Mass Number given a IMolecularFormula (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Added copyright info (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Added missing dep (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Rearranged the order of operations and provided a useful message. Added bug annotation (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Updated test to check that a aromatic molecle coming from two diferent sources (kekule and aromatic SMILES) gets represented internally as the same thing. Currently does not (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * removed "throws CDKException" from method StructureResonanceGenerator.setReactions(List<IReactionProcess> newReactionsList). And depending methods as StabilizationCharges.calculatePositive. It was producing some incoherences: org.openscience.cdk.charges.StabilizationCharges row 83: Unreachable catch block for CDKException. This exception is never thrown from the try statement body. (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Fixed a bunch of Javadoc errors (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Added method to IAtomTypeMatcher to perceive types for all atoms in the container; allowing some removal of redundant calculations, and the addition of calculation of molecular properties, like aromaticity, as used in the Sybyl atom type matcher (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * added a convenience constructor to smilesgenerator, improved a test to test the aromaticity behaviour (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Fixed copyright notice for 2009 (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Fixed duplicate storage of layout templates, which only belong in the sdg module, not extra module too (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * used interfaces where possible and updated to 1.5 idioms (Rajarshi Guha <rguha@localhost.localdomain>) | ||
| * Updated to use interfaces where possible and cleaned up code to use 1.5 idioms (Rajarshi Guha <rguha@localhost.localdomain>) | ||
| * Added unit test for a ONS Solubility solute, which fails to be parsed when RDF. But does not fail here. (egonw <egon.willighagen@gmail.com>) | ||
| * Export the jniinchi lib (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Fixed a few test class instantiation problems (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Fixed constructor: wrong file format; add getClassLoader() (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Fixed for NewCDKTestCase -> CDKTestCase renaming (Egon Willighagen <egon.willighagen@gmail.com>) | ||
| * Added all existent reaction tests in MreactionTest (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Added dictionary which reads from a reaction-process.owl the mechanism for specific type reaction. (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Invalid smiles string (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Set new methods to read new schemes of the reactions dictionary (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * Added testMethod value for Junit4 (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>) | ||
| * For each data class, also test inherited methods for super classes implementing inherited superinterfaces (Egon Willighagen <egon.willighagen@gmail.com>) |