Merge branch 'release-3.1.0'

doc/html/_sources/core/runtime_profiling.txt

doc/html/_sources/core/setcompoundschemlib.txt

doc/html/_sources/dev_setup.txt

doc/html/_sources/developers.txt

doc/html/_sources/gettingstarted.txt

doc/html/_sources/index.txt

doc/html/_sources/license.txt

doc/html/_sources/loop/all_atom.txt

doc/html/_sources/loop/backbone.txt

doc/html/_sources/loop/index.txt

doc/html/_sources/loop/load_loop_objects.txt

doc/html/_sources/loop/mm_system_creation.txt

doc/html/_sources/loop/structure_db.txt

doc/html/_sources/loop/torsion_sampler.txt

doc/html/_sources/modelling/algorithms.txt

doc/html/_sources/modelling/gap_handling.txt

doc/html/_sources/modelling/index.txt

doc/html/_sources/modelling/loop_candidates.txt

doc/html/_sources/modelling/loop_closing.txt

doc/html/_sources/modelling/model_checking.txt