Merging vmullig/cycpep into master to bring in a number of important changes:
--Certain residue types have been updated (sidechain-conjugation types and crosslinker types) and new ones added. Note that the new residue types are OFF by default in residue_types.txt (as they should be!)
--Wendao's BBG mover is a part of this branch.
--Improvements to the logic for adding residues by bond, jumps, etc., needed for building complicated cyclic peptides.
--Improper dihedrals added to residue types.
--Considerable improvements to the PeptideStubMover, GeneralizedKIC, and other tools for modelling complicated cyclic peptides.
--Support added to SilentFilePoseInputStreams for loading poses in the order in which they appear in a file, instead of in alphabetical order of tags.
--Added a flag to force big-endian/little-endian flipping on binary silent file read (for cases in which automatic detection fails).
--A few pilot apps have been added, including bettercluster.cc, design_cycpeptide_MPI.cc, and PCA_visualizer.cc.
Unit test status: ALL PASS (prior to merging master -> vmullig/cycpep, since the current master already has three broken unit tests)
Integration test status: 6 changed tests, all with expected changes
FAIL UBQ_E2_thioester_extra_bodies
--Uses the sidechain-conjugation residue types, which have been updated.
FAIL ligand_dock_script
--Seems to be a numeric precision issue, not a true failure.
FAIL UBQ_E2_thioester
--Uses the sidechain-conjugation residue types, which have been updated.
FAIL UBQ_Gp_LYX-Cterm
--Uses the sidechain-conjugation residue types, which have been updated.
FAIL broker
--Trivial change to output messages when binary silent file big-endian/little-endian flipping occurs.
FAIL UBQ_E2_thioester_two_ubiquitins
--Uses the sidechain-conjugation residue types, which have been updated.
modified: database/chemical/residue_type_sets/fa_standard/patches/N_acetylated.txt
modified: database/chemical/residue_type_sets/fa_standard/residue_types.txt
new file: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.2_bisbromomethylbenzene.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.3_bisbromomethylbenzene.params
new file: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.4_bisbromomethylbenzene.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/BoronateLDopa.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/ASX.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/CYX.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/LYX.params
new file: source/src/apps/pilot/vmullig/PCA_visualizer.cc
new file: source/src/apps/pilot/vmullig/alglib/alglibinternal.cpp
new file: source/src/apps/pilot/vmullig/alglib/alglibinternal.h
new file: source/src/apps/pilot/vmullig/alglib/alglibmisc.cpp
new file: source/src/apps/pilot/vmullig/alglib/alglibmisc.h
new file: source/src/apps/pilot/vmullig/alglib/ap.cpp
new file: source/src/apps/pilot/vmullig/alglib/ap.h
new file: source/src/apps/pilot/vmullig/alglib/dataanalysis.cpp
new file: source/src/apps/pilot/vmullig/alglib/dataanalysis.h
new file: source/src/apps/pilot/vmullig/alglib/diffequations.cpp
new file: source/src/apps/pilot/vmullig/alglib/diffequations.h
new file: source/src/apps/pilot/vmullig/alglib/fasttransforms.cpp
new file: source/src/apps/pilot/vmullig/alglib/fasttransforms.h
new file: source/src/apps/pilot/vmullig/alglib/integration.cpp
new file: source/src/apps/pilot/vmullig/alglib/integration.h
new file: source/src/apps/pilot/vmullig/alglib/interpolation.cpp
new file: source/src/apps/pilot/vmullig/alglib/interpolation.h
new file: source/src/apps/pilot/vmullig/alglib/linalg.cpp
new file: source/src/apps/pilot/vmullig/alglib/linalg.h
new file: source/src/apps/pilot/vmullig/alglib/optimization.cpp
new file: source/src/apps/pilot/vmullig/alglib/optimization.h
new file: source/src/apps/pilot/vmullig/alglib/solvers.cpp
new file: source/src/apps/pilot/vmullig/alglib/solvers.h
new file: source/src/apps/pilot/vmullig/alglib/specialfunctions.cpp
new file: source/src/apps/pilot/vmullig/alglib/specialfunctions.h
new file: source/src/apps/pilot/vmullig/alglib/statistics.cpp
new file: source/src/apps/pilot/vmullig/alglib/statistics.h
new file: source/src/apps/pilot/vmullig/alglib/stdafx.h
new file: source/src/apps/pilot/vmullig/bettercluster.cc
new file: source/src/apps/pilot/vmullig/design_cycpeptide_MPI.cc
modified: source/src/apps/pilot/wendao/test_bbmc.cc
modified: source/src/basic/options/options_rosetta.py
modified: source/src/core/chemical/ResidueType.cc
modified: source/src/core/chemical/ResidueType.hh
modified: source/src/core/conformation/Conformation.cc
modified: source/src/core/conformation/Conformation.hh
modified: source/src/core/conformation/Residue.cc
modified: source/src/core/import_pose/pose_stream/SilentFilePoseInputStream.hh
modified: source/src/core/import_pose/pose_stream/util.cc
modified: source/src/core/import_pose/pose_stream/util.hh
modified: source/src/core/io/silent/BinarySilentStruct.cc
modified: source/src/core/io/silent/SilentFileData.cc
modified: source/src/core/io/silent/SilentFileData.hh
modified: source/src/core/io/silent/SilentStruct.cc
modified: source/src/core/io/silent/SilentStruct.hh
modified: source/src/core/kinematics/FoldTree.cc
modified: source/src/core/kinematics/FoldTree.hh
modified: source/src/core/pose/Pose.cc
modified: source/src/core/pose/Pose.hh
modified: source/src/pilot_apps.src.settings.all
modified: source/src/protocols/cyclic_peptide/CreateAngleConstraint.cc
modified: source/src/protocols/cyclic_peptide/CreateAngleConstraint.hh
modified: source/src/protocols/cyclic_peptide/CreateDistanceConstraint.cc
modified: source/src/protocols/cyclic_peptide/CreateDistanceConstraint.hh
modified: source/src/protocols/cyclic_peptide/CreateTorsionConstraint.cc
modified: source/src/protocols/cyclic_peptide/CreateTorsionConstraint.hh
modified: source/src/protocols/cyclic_peptide/PeptideStubMover.cc
modified: source/src/protocols/cyclic_peptide/PeptideStubMover.hh
modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc
modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.hh
modified: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc
modified: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.hh
modified: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc
modified: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.hh
modified: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.cc
modified: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.hh
modified: source/src/protocols/generalized_kinematic_closure/util.cc
modified: source/src/protocols/simple_moves/BBConRotMover.cc
modified: source/src/protocols/simple_moves/BBConRotMover.hh
modified: source/src/protocols/simple_moves/BBGaussianMover.cc
modified: source/src/protocols/simple_moves/BBGaussianMover.hh