rajarshi (Rajarshi Guha)

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 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

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.

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.

Added the Mannhold LogP descriptor to the ontology

Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations

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