evaluator for contact and site graphs restored
merged with master
src/main/scala/kappa/immutable removed
pattern builder and less assumptions
KaSpace Parser/LanguageContext/Symbols/Patterns are working
documentation added to :@ and !@
parse inverse link states and split off the language-specific parts from the parser
splitted off Kappa and KaSpace specific parts from LanguageContext
contact graph removed from constructor and put in a setter
added KaSpace proteasome model
merged with sast
Merge branch 'sast' into rhz
little things
Merge branch 'rhz' of https://github.com/sstucki/lms-kappa into rhz
fixes after merge
Adds geometric soundness check.  Test model does not work as expected due to missing link geometries.
Introduces approximate comparisons of positions/orientations and fixes NPE in Mixture rollback.
Fixes bug in merge method of ComponentBuilder.
Adds better support for mixture initialization.
Fixes bugs and adds observables in TestKaSpaceModel.