CDK 2.12

Version 2.12 of the Chemistry Development Kit has been released. It is the last release with contributions by our NWO Open Science grant. This release adds some nice new APIs:

• harmonize hydrogens to various states: depiction, stereo, minimal, and unsafe (useful for depictions)
• generate wedge bonds based on coordinates and stereochemistry
• more Markush / RGroup support
• atropisomers via CXSMILES
• sugar extraction

I also update the following libraries/tools to use CDK 2.12:

• NanoJava 2.16
• Bacting 1.0.10 (and the Python pyBacting will follow asap)