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Tuesday, May 25, 2010

CDK 1.3.5

A lot of changes in this release: the SMSD code (see doi:10.1186/1758-2946-1-12), removed outdated code (force field, R-CDK bridge), SMILES @ and @@ chiralities reading, a new IChemObjectBuilder interfaces, and several new features in the MDL IO classes. The full list:
  • Fix for getBestAlignmentForLabelXY eb7529b
  • Test for getBestAlignmentForLabelXY 2cb5f4d
  • Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality d80628e
  • fixed PMD errors on Use instanceof against interfaces not implementations and few more Signed-off-by: Syed Asad Rahman e36a2a1
  • Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality 3043c17
  • Introducing PMD test for CDK specific issues: 406930b
  • Removed unstable forcefield code 235b04f
  • Added copyright and license header d6b6c65
  • 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 2399a18
  • updated test cases Signed-off-by: Syed Asad Rahman 32cb936
  • add on patches 4bdce61
  • fixed makeAtomsMapOfBondsMap with test 5bd8d64
  • Emergency fix: IAminoAcid instead of AminoAcid 5193626
  • A few more interfaces instead of implementations 648a2f4
  • Replaced use of implementations by interfaces 6317be2
  • Use an interface instead of an implementation as type b82a2f6
  • Use interfaces instead of implementation 50b9e74
  • MDL reading and writing atom value line, including test cases c88bd3c
  • Added another test to check that a query larger than the target does not match 088afce
  • Test cases for MCS updated 15fa35a
  • updated MCS solution count in the VF lib, depricated turbo MCS and provided methods for timeout c4d3bf9
  • updated test for single atom ed04f25
  • Replaced outdated URL with entry in WikiPedia (fixes #3002741) ad2bd3e
  • Fixed outdated JavaDoc I forgot to remove (fixes #3002409) 82f40a1
  • Included the qm module in the dist-all (fixes #3002622) e2c95ec
  • Cleaned up unthrown exceptions 2501371
  • Removed use of SMARTS parser in the test code so that a new dependency is not required e561364
  • removed unwated checks 41561a2
  • commented unused code f39566c
  • test cases for the IQueryAtomContainer support in the SMSD with exceptions fixed 839827b
  • test cases for the IQueryAtomContainer support in the SMSD b292f7c
  • IQuery* support for the SMSD, will help in SMART based searches 75d86dd
  • Turbomode MCS search added f3f809e
  • Turbo mode MCS search added Signed-off-by: Syed Asad Rahman 8ac67bf
  • removed unwanted test case Signed-off-by: Syed Asad Rahman ea4960c
  • VF Sub search turbo mode 5b4f00a
  • Updated the SMSD code for turbo mode substructure search Refactored the SMSD class itself f5ccf1b
  • 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 9cbc242
  • Added two more unit tests, related to ring closing 0f4649c
  • SMILES @ and @@ chiralities are now fully read. 2dd575e
  • Added unit tests with various chiral SMILES situations. 4c2e9b7
  • Implemented stereo chemistry for atoms with four ligands 9abead5
  • Patch to generalize the stereo chemistry handling. be1b70a
  • Minor fix to build.xml to ensure that SMSD code gets included in the large jar file ee5e0a2
  • Added JavaDoc testing to the QA task; removed module-uptodate which checked if the module was already compiled causing the target to be skipped a1e1f1b
  • 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. 42b64e1
  • The RXNReaders/Writers now all handle Atom-Atom-Mappings. This was only done in the MDLRXNReader till now 6ff55ba
  • 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. 6b787c2
  • Flexibility for ring start angles. d6d6ab0
  • more mdl reader writer tests 353f938
  • Revert "Additional constant" 3b974e6
  • Added a test case for short line mol files. Patch by S.Kuhn, reworked by M.Rijnbeek. c4ea1d8
  • MDL reading and writing UP_OR_DOWN e36983b
  • Removal of references to removed R-CDK bridge fd1e57c
  • Removed the R-based model package and associated jar files and test code 5733da3
  • Removal of references to removed R-CDK bridge b1075d7
  • Removed the R-based model package and associated jar files and test code e41372b
  • Removal of references to removed R-CDK bridge d3f65d0
  • Removed DocCheck from Eclipse' Build Path fcd7623
  • Removed obsolete castings, or replaced by more general ones b34423d
  • added @Test Signed-off-by: Syed Asad Rahman eebdb3d
  • added CDKRMapHandlerTest 82b9faf
  • added CDKRMapHandlerTest Signed-off-by: Syed Asad Rahman bb7bcb4
  • The big SMSD patch. 10edb71
  • Fixed a ClassCastException in a unit test; I messed up (mea culpa) b5fa3dc
  • 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) 25427b4
  • Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors 5f34897
  • Added missing cloning of single electrons 2d4c122
  • Do not try to clone the atom if it does not exist 9672df0
  • MDL reading and writing valency c20a0ea
  • Line separator fix for RGroup writer ad706cc
  • de-Javadoc numerous comments (fixes #2980066) 4fc4837
  • More extensive testing for removeHydrogens in atomcontainers with hetero atoms without Hs 3155d7d
  • Be a bit more forthcoming with debug messages: report also the parameter types of the method 0f85f52
  • 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. 708cf8a
  • converted uses of indexOf to startsWith/contains 7b9d84e
  • Updated HIN reader to fix bug 2984581 f95c632
  • Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten 38d5f8d
  • Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original 3c1b07e
  • Removed duplication of cloning. 216c160
  • 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. 4e5d6a1
  • Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too 068fb3b
  • Fixed a typo in the test method name 8142ae5
  • Got rid of some debug prints 6079160
  • Fixed a regex bug which prevented the engine from properly loading descriptor class names 9bd0490
  • Some code cleanup to make it more idiomatic Java 565d7c3
  • New IChemObjectBuilder interface: 45f683f
  • 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 3be2367