Including latest updates to Environment system, including improved unit test coverage, improved virtual residue handling, residue selector use, and numerous bug fixes. Trivial log integration test changes expected in all rosetta scripts applications.
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Fixing unit tests that were affected by the MAX_RESIDUE_TYPE limit.
Nine core unit tests and one protocols unit test have actually been "silently" failing due to the new max residue types limit.
The patches.txt file has recently been edited to cut down on the number of ResidueTypes created and a limit of 3000 ResidueTypes has been set on the size of the ResidueTypeSet (limit is controllable from the options system). Only the fa_standard/patches.txt was edited however. Tests that call the -restore_pre_talaris_2013_behavior flag don't observe the changes to fa_standard/patches.txt were affected by the limit on the ResidueTypeSet. They hit the limit and then utility_exit. For some reason, they not register as failing.
Unit test status: [All Pass except for DdgFilter on linux gcc]
Integration test status: [No test changes expected]
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Removing duplicated virtualBB.txt patch from patches.txt
This should fix the rotamer recovery unit test. I am not sure why the unit tests did not skip the patch like the integration tests do. I suspect the ResidueTypeSet is construcutred differently in the unit tests.
Unit test status: [All test pass except DDG tests that are currently failing still fail]
Integration test status: [11]
10 cosmetic integration tests changes relating to virtualBB.txt no longer being skipped.
What looked like rounding differences in the ligand docking integration test occured on my system.
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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
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Updating LoopAnchorFetures and related scripts.
The features integration tests will change because both the schema and what is being computed has changed.
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