Merge branch 'release-3.1.1'

doc/html/_sources/modelling/loop_closing.rst.txt

doc/html/_sources/modelling/model_checking.rst.txt

doc/html/_sources/modelling/monte_carlo.rst.txt

doc/html/_sources/modelling/pipeline.rst.txt

doc/html/_sources/modelling/sidechain_reconstruction.rst.txt

doc/html/_sources/portableIO.rst.txt

doc/html/_sources/references.rst.txt

doc/html/_sources/scoring/all_atom_scorers.rst.txt

doc/html/_sources/scoring/backbone_score_env.rst.txt

doc/html/_sources/scoring/backbone_scorers.rst.txt

doc/html/_sources/scoring/index.rst.txt

doc/html/_sources/scoring/other_scoring_functions.rst.txt

doc/html/_sources/sidechain/disulfid.rst.txt

doc/html/_sources/sidechain/frame.rst.txt

doc/html/_sources/sidechain/graph.rst.txt

doc/html/_sources/sidechain/index.rst.txt

doc/html/_sources/sidechain/loading.rst.txt

doc/html/_sources/sidechain/rotamer.rst.txt

doc/html/_sources/sidechain/rotamer_constructor.rst.txt

doc/html/_sources/sidechain/rotamer_lib.rst.txt