Skip to content

Commit

Permalink
Added changes for 1.3.4 and 1.3.5
Browse files Browse the repository at this point in the history
  • Loading branch information
@egonw
egonw committed May 25, 2010
1 parent 60a3929 commit 8a8f443
Showing 1 changed file with 122 additions and 1 deletion.
123 changes: 122 additions & 1 deletion changelog.txt
View file
Expand Up @@ -400,4 +400,125 @@ This changelog is automatically generated from the:
* Moved IAtomColorer and ICDKChangeListener from the standard module to the interfaces module (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated to include the float and binary information found in PubChem (Brian Gilman <gilmanb@gmail.com>)
* Ant has a release 1.8 that should be accepted in build.xml (Mark Rynbeek <markr@localhost.localdomain>)
* Master is open for patches... (Egon Willighagen <egonw@users.sourceforge.net>)
* Master is open for patches... (Egon Willighagen <egonw@users.sourceforge.net>)

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

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

0 comments on commit 8a8f443

Please sign in to comment.