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Chemistry Development Kit Changelog

What's new in Chemistry Development Kit 1.3.3

May 30, 2011
  • Updated JavaDoc to explicitly state that g2 must be a substructure of g1
  • More unit tests for the MCSS problem in bug report 2944080.
  • Simplified the code using the new 'T read(T)' API used in MDLV2000Reader as defined by the ISimpleChemObjectReader
  • Updated for the new generics 'T read(T)' API in ISimpleChemObjectReader.
  • 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.
  • Added missing dependency, fixing the unit test reading a file from data /
  • added working implementations for PartialFilledStructureMerger and CrossoverMachine
  • added working implementations for PartialFilledStructureMerger and CrossoverMachine
  • tests for crossover machine and PartialFilledStructureMerger
  • tests for crossover machine and PartialFilledStructureMerger
  • added dependency
  • Fixed use of global isRef variable, to make it threading-safe
  • Added control 'isref' creating a CML with reaction and list molecules
  • Removed unused import
  • Removed last bits of implementation details from the API: now uses List instead of ArrayList
  • Removed output to STDOUT
  • Fixed some spelling errors and added JavaDoc links
  • Synchronized behavior with the MDLV2000Reader
  • Added missing @cdk.bug tag and used interfaces where possible
  • 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.
  • added a method to make cyclopentane to MoleculeFactory
  • Added missing unit test for getClosestAtom(double, double, IAtomContainer, IAtom)
  • 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.
  • Added a unit test to see of the calculated bond length average includes bonds in all IAtomContainer's
  • Added second test for getClosestAtom(), now with more than two atoms
  • Added E and Z as allowed configurations
  • Added UP_OR_DOWN_INVERTED, which is the equivalent of UP_OR_DOWN but with a different stereocenter
  • Extended JavaDoc, explaining how these IBond. Stereo types define the stereo center, and indicating for each type explicitly which atom is the stereo center
  • Added convenience method to find the closest atom to a given point.
  • unified the layout at cleanup and loading of molecules
  • Reimplemented shiftReactionVertical(IReaction, Rectangle2D, Rectange2D, double)
  • Added a getBondLengthAverage(IReaction reaction) method
  • Add a GeometryTools method to get atoms near another atom. Added unit test for the new method.
  • Moved IAtomColorer and ICDKChangeListener from the standard module to the interfaces module.
  • Updated to include the float and binary information found in PubChem.
  • Ant has a release 1.8 that should be accepted in build.xml
  • Master is open for patches.

New in Chemistry Development Kit 1.3.2 (May 30, 2011)

  • * 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.
  • * Merged with 1.2.x
  • * The IMapping interface had a class comment which probably was a copy&paste artefact. Changed this.
  • * Fixed license info .meta file for JavaCC
  • * Merged CDK 1.2.5
  • * Bumped version to differ form the 1.2.5 release
  • * Release 1.2.5
  • * 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
  • * Added changelog for 1.3.1
  • * Merged in 1.2.4.1
  • * Bumped version to denote post 1.2.4.1
  • * 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
  • Branch open for patches after 1.3.1 ...
  • Added some extra lines, hopefully fixing the conflicts all the time
  • Bumped version number to distinguish from the 1.2.4 release

New in Chemistry Development Kit 1.3.1 (Dec 11, 2009)

  • Bumped version for 1.3.1 release
  • Added some extra lines, hopefully fixing the conflicts all the time
  • Fixed param name
  • Updated the makefp3d target to work with the current build system
  • Set up a branch for the 1.2.4 release
  • 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.
  • Added tests to match hydrogens
  • Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator
  • Reworked the tests for bug 2898032. Updated Javadocs for smiles generator
  • Added unit test to confirm and check for bug 2898032
  • Fixed junior issue 1802586: Misuse of assertTrue for tested strings
  • Made the AtomContainerPermutors IAtomContainer implementation independent
  • 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
  • Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch
  • Implemented instantiating custom loggers; example in the unit test class
  • Added the use of the SystemOutLoggingTool as back up
  • Added a ILoggerTool implementation for STDOUT
  • Dig up and updated the copyright history
  • Factored out initialization of the tool, to allow reusing the code for other logger class names
  • Moved the log4j.jar depending LoggingTool into a separate module
  • 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.
  • Added generation of java source jars
  • Fixed matchers to allow XML without new lines (closes #2832835)
  • Added unit tests for detection of PubChem XML files.
  • Fixed matchers to allow XML without new lines (closes #2832835)
  • Added unit tests for detection of PubChem XML files.
  • Added reading of E/Z stereochemistry from double bonds in MDL V2000 molfiles.
  • A minor fix to clean up a PDMD warning
  • Overwrite unit tests, because there are no change events passed around at all for the NoNotification interface implementations
  • Added missing unit tests for IChemModel event propagation for the ICrystal field
  • Fixed propagation of change events to IChemModel when modifications are made in child IChemObjects
  • 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.
  • Synchronized with the Blue Obelisk version
  • Added unit test to the function of the new IO setting to force 2D coordinate output.
  • Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted.
  • Added unit test to verify that if 2D and 3D coordinates are available, the 3D coordinates are outputted.
  • Changed IBond.get/setStereo() to use a IBond.Stereo enumeration instead of an int (fixes #2855850):
  • 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
  • Added the Mannhold LogP descriptor
  • Added the Mannhold LogP descriptor to the ontology
  • 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
  • Fixes ClassCastException when not IMolecule
  • Upgraded to PMD 2.4.5 with many bug fixes, giving more accurate error reports
  • Added missing dependency on cdk-diff, being used in one of the unit tests
  • Fixed methods names to match those in the test class
  • Fixed test method name to match the expected patters, fixing a coverage test fail
  • Removed duplicate code: MolecularFormulaTest now extends AbstractMolecularFormulaTest
  • Fixed test method annotation to point to the right method
  • Added missing @TestMethod annotation
  • Added modules that were missing from the PMD testing
  • Added modules that were missing from the doccheck testing
  • Added reference to IUPAC documentation about stereochemistry visualization.
  • Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG
  • Added missing dependency introduced by the use of AbstractFingerprinterTest in test-standard.
  • Updated the unit test classes for all IFingerprinter implementations to use the new AbstractFingerprinter class; a few unit tests actually fail
  • Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations
  • Clean up of layout.
  • Fix the unit test to not give a 'input must support mark' exception on some platforms, by wrapping the InputStream in a BufferedInputStream.
  • Added missing dependencies
  • Added ioformats to modules to test
  • Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where multiline field data is found.
  • 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
  • Factored out steps in reading the SD file data block
  • Bumped version, to make it clear this is not the 1.2.3 release
  • Bumped version, to make it clear this is not the 1.3.0 release
  • Fixed registering on the cdk.threadnonsage tag (closes #2796362)
  • Removed obsolete pattern from old svnrev tag
  • Fixed JavaDoc to remove traces of the old svnrev Tag
  • Synchronized exception message with implementation (fixes #2844333)
  • Made class private again, per authors request
  • Any class will do, not just public, final and abstract
  • Two further compile fixes after the merge with CDK 1.2.x
  • Made the class public, to fix a compile problem introduced by the merge with CDK 1.2.x
  • Added ant task to calculate JavaNCSS code statistics
  • Added JavaNCSS 32.53 (LGPL 3.0)
  • The Pauling Electronegativity is copied in configure as well. I can't see why not copy everything we have.
  • Revert "added a test for bug 2831420":
  • Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG
  • added a test for bug 2831420
  • added a test for bug #2831420
  • Made InChIGeneratorFactory a singleton.
  • Layout.
  • Added bug annotation
  • test case for bug #2846213
  • Fixed perception of N.planar3 where N.sp2 was detected, by now taking into account the given hydrogen count.
  • 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.
  • Added assertions to unit test for values being not null
  • 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.
  • 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.
  • Unsealed the XOM jar to allow having the CustomSerializer
  • Fixed Javadocs error
  • Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag
  • Added support for 'public enum's
  • 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)
  • added a new test for bondtools
  • Fixed inconsistency between accepts() and write: also support writing of IAtomContainerSet and IAtomContainer as accepts() indicates (fixes #2827745)
  • General test for testing consistency between write() and accepts(), testing that all accepted IChemObject's can also be written
  • Added unit test for bug #2826961: inconsistent atom typing for two SMILES. Unit test does not show a fail, ruling out a CDK bug
  • Remove erroneous throws statement
  • Bug found calculating the exact mass given a molecular formula when it is negative charged.
  • Fixed reading of the cdk/dict/data/elements.owl database which is now in OWL
  • Fixed issue 2458210: use assertNotNull(foo) etc instead of assertTrue(foo != null).
  • Added minimum equivalents for BondManipulator.getMaximumBondOrder() methods
  • Fixes asserts: after removal *no* change should be recorded
  • Added IO option to disable generator of XML declaration statements in the output CML.
  • Added generics, and consistified code by always returning a List of the same '?'. (And some 80 chars fixes in the JavaDocs.)