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A lot of changes in this release: the SMSD code (see doi:10.1186/1758-2946-1-12), removed outdated code (force field, R-CDK bridge), SMILES @ and @@ chiralities reading, a new IChemObjectBuilder interfaces, and several new features in the MDL IO classes.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 eb7529b4aa

Test for getBestAlignmentForLabelXY 2cb5f4d5a9

Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality d80628ef4c

fixed PMD errors on Use instanceof against interfaces not implementations and few more Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> e36a2a122e

Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality 3043c177b6

Merge branch 'cdk-1.2.x' b8110ae58d

Introducing PMD test for CDK specific issues: 406930b292

Removed unstable forcefield code 235b04fd3c

Added copyright and license header d6b6c65f5a

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 2399a18ba3

updated test cases Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> 32cb936040

add on patches 4bdce612cd

fixed makeAtomsMapOfBondsMap with test 5bd8d64f62

Emergency fix: IAminoAcid instead of AminoAcid 5193626538

Merge branch 'cdk-1.2.x' 2f56fd6ddb

A few more interfaces instead of implementations 648a2f48b8

Replaced use of implementations by interfaces 6317be25ed

Use an interface instead of an implementation as type b82a2f69be

Use interfaces instead of implementation 50b9e74182

MDL reading and writing atom value line, including test cases c88bd3c0d4

Added another test to check that a query larger than the target does not match 088afcedde

Test cases for MCS updated 15fa35a769

updated MCS solution count in the VF lib, depricated turbo MCS and provided methods for timeout c4d3bf9cad

updated test for single atom ed04f25218

Replaced outdated URL with entry in WikiPedia (fixes #3002741) ad2bd3ed63

Fixed outdated JavaDoc I forgot to remove (fixes #3002409) 82f40a1efd

Included the qm module in the dist-all (fixes #3002622) e2c95ec1dc

Cleaned up unthrown exceptions 2501371362

Removed use of SMARTS parser in the test code so that a new dependency is not required e561364152

removed unwated checks 41561a25f4

commented unused code f39566c797

test cases for the IQueryAtomContainer support in the SMSD with exceptions fixed 839827b873

test cases for the IQueryAtomContainer support in the SMSD b292f7c795

IQuery* support for the SMSD, will help in SMART based searches 75d86dd0fc

Merge branch 'master' of git@github.com:cdk/cdk 6d1a730700

Turbomode MCS search added f3f809ed50

Turbo mode MCS search added Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> 8ac67bf99e

removed unwanted test case Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> ea4960cda6

VF Sub search turbo mode 5b4f00a63b

Updated the SMSD code for turbo mode substructure search Refactored the SMSD class itself f5ccf1bdc8

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 9cbc242454

Added two more unit tests, related to ring closing 0f4649c0d0

SMILES @ and @@ chiralities are now fully read. 2dd575ed56

Added unit tests with various chiral SMILES situations. 4c2e9b7a96

Implemented stereo chemistry for atoms with four ligands 9abead553d

Patch to generalize the stereo chemistry handling. be1b70ac15

Merge branch 'master' of git://github.com/egonw/cdk 1d5a29bfd8

Minor fix to build.xml to ensure that SMSD code gets included in the large jar file ee5e0a21c3

Added JavaDoc testing to the QA task; removed module-uptodate which checked if the module was already compiled causing the target to be skipped a1e1f1b78f

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. 42b64e1341

The RXNReaders/Writers now all handle Atom-Atom-Mappings. This was only done in the MDLRXNReader till now 6ff55baf51

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. 6b787c2fd6

Flexibility for ring start angles. d6d6ab0022