Chemistry Development Kit 1.4.1

Java library for bio- / chemoInformatics and computational chemistry Chemistry Development Kit is now developed by more than 40 developers all over the world and used in more than 10 different academic as well as industrial projects world wide. In the past four years, the CDK library evolved into a fully blown chemoinformatics package with code reaching from QSAR descriptor calculations to 2D and 3D model building. Programs like the 2D structure editor NMRShiftDB and JChemPaint, a database of organic molecules and their NMR spectra are based on the Chemistry Development Kit (CDK). · Read and write chemical data formats · Render chemical structures · Algorithms for chemical graph theory · QSAR descriptors Requirements: · Java · Updated JavaDoc to explicitly state that g2 must be a substructure of g1 · More unit tests for the MCSS problem in bug report 2944080. · Simplified the code using the new ‘T read(T)’ API used in MDLV2000Reader as defined by the ISimpleChemObjectReader · Updated for the new generics ‘T read(T)’ API in ISimpleChemObjectReader. · Introduced generics allowing the return type to be identical to the passed argument. It does require implementing classes to be updated with the new API too. · Added missing dependency, fixing the unit test reading a file from data / · added working implementations for PartialFilledStructureMerger and CrossoverMachine · added working implementations for PartialFilledStructureMerger and CrossoverMachine · tests for crossover machine and PartialFilledStructureMerger · tests for crossover machine and PartialFilledStructureMerger · added dependency · Fixed use of global isRef variable, to make it threading-safe · Added control ‘isref’ creating a CML with reaction and list molecules · R…