release candidate for publication

Major code update and clean-up of commandline parameters

• DrTransformer.py:
  • added new plotting function (--xmgrace)
  • repaired existing matplotlib plots (--pyplot)
  • uses treekin-v0.4.1 for more robust kinetic simulations
  • uses fallback mode crnsimulator-v0.1 for kinetic simulations if treekin breaks.
  • supports different STDOUT output modes
  • --structure-search-mode for more control over neighborhood generation
  • ...and many more little interface changes
• BarMap.py:
  • various bug-fixes and adaptations due to library interface changes
• cofold_kinetics.py and pylands_spatch.py:
  • have been temporarily removed from system-wide installations. They are not production-ready.

PhD Thesis version

This version has been used to study cotranscriptional folding and kinetics of interacting RNAs in:

Stefan Badelt, "Control of RNA function by conformational design", (2016), PhD Thesis, University of Vienna