Dummy commit to trigger server run

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Add missing Dumbrack-binary-generating exclusion to the integration test ignore list.

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Merge pull request #1703 from RosettaCommons/aleaverfay/fix_mpm_premature_parsing The MPM's parse_my_tag function would exit/segfault if one of the inner objects being parsed needs to look at the Pose because the MPM was giving it an empty Pose. Previously, during parse_my_tag, the MultiplePoseMover would create (and then dispose of) a Mover for the inner parsed protocol. The rationale for this was to avoid the "die_for_unaccessed_options" behavior of Tag called by the outer ParsedProtocol. The idea was: go ahead and parse the inner set of Movers and Filters, and thereby read any and all options. Any un-read option would be found as the outer parsed protocol wrapped up. To create this temporary parsed protocol, the MultiplePoseMover created an empty Pose and passed it into the parsing of the inner parsed protocol. This empty Pose presents a problem, however, if a Mover in the inner parsed protocol wants to look at the first residue in chain 2. There is no chain 2! There isn't a chain 1! In this new implementation, the MultiplePoseMover simply marks all options of the input tag as read, to avoid the "die_for_unaccessed_options" behavior. During its apply function, if there are unaccessed options, then it will discover that, and exit. Oh, what a time to realize that there was a problem with your XML file! Imagine running a job for 24 hours, to have it die in the last 10 minutes because you spelled "scorefxn" wrong! It's still better, though, than taking the bad output and ordering genes, and wasting 3 months at the bench on a poor design. This fixes the bug that Franziska saw with an inner FastRelax mover that contains a MoveMap. (Incidentally, the move-map reading code really should do error checking on the input tags instead of seg faulting!)

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Merge pull request #1746 Adding sorting to list_dir implementation to improve Rosetta result stability

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Merge pull request #1322 from RosettaCommons/roccomoretti/ddg_nonprot An old pull request which attempted to fix issues with non-protein residues in ddg_monomer and associated. Some of these were fixed in a separate pull request (#1465) from Amelie. These are residual fixes/tweaks that aren't superflous from those.

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Merge pull request #1744 from RosettaCommons/dougrenfrew/optE_override Adding additional overrides to OptE code when compiling with MPI

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Merge pull request #1221 from RosettaCommons/roccomoretti/cst_output Add Constraint info application and mover So you've generated a bunch of models, and you want to see how well they match the constraints. Certainly you can get the complete constraint score, but what if you want to know how each constraint behaves? This pull request adds a mover and an application which will take one or more constraint files and one or more input structures, and will produces an output table of each constraint and subconstraint (for nested constraints like Ambigious and KofN constraints) regarding a) what their score is, and b) what is the metric prior to function application. The RosettaScripts interface can also be set to report on the constraints that are currently in the pose. There's a slight change to the Constraint object interface to enable (and enforce) the ability to do this.

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Cartoon mode fix changing normalize(15) to normalize(), otherwise the width of cartoon sheets/helices is messed up!

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Merge pull request #1741 from RosettaCommons/xingjiepan/improve_refactoredKIC_performance Xingjiepan/improve refactored kic performance

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Merge pull request #1740 Updating profile test script so it now check if ‘command’ file is present in test dir.

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Merge pull request #1726 from RosettaCommons/roccomoretti/rosie_ligdoc_memory_issue Add memory tests for ROSIE ligand docking The ligand docking updates to ROSIE were suffering from memory issues, due to -restore_pre_talaris_2013_behavior usage and the old Etables scheme. This pull request corrects that in the integration test copy of the protocol. It also adds a profile test version, which should catch if memory issues sneak back in. I've also removed the ligand_dock_script profile test, as ligand docking was now covered by three profile tests, and rosie_ligand_dock is the new, recommended equivalent of ligand_dock_script.

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Merge pull request #1737 from RosettaCommons/roccomoretti/gcc_with_inf Change compile settings to allow NaN/Inf Current settings for GCC and MSVC enable "fast math", which as part of their optimizations allow the compiler to assume that IEEE-754 NAN and INF values aren't generated. This is a problem, as there are a number of places in Rosetta which explicitly test for NaN/Inf, and these optimizations mean that these tests aren't doing what people think they are in release mode. (Note that clang does not have a "fast math" setting, or at least one that we enable, so it is immune to these issues.) This adds the -fno-finite-math-only flag to the GCC settings, which tells GCC to keep proper NaN/Inf support. (I'm disabling /fp:fast in MSVC, as it doesn't appear that MSVC has fine grain control of the fast math options.) This pull request also attempts to centralize the isnan/isinf handling in the code (to the functions in src/utility/numbers.hh), so we can better use robust methods if we do need to make an adjustment.

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Merge pull request #1156 from RosettaCommons/sboyken/hbnet2master Merge HBNet into master

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Merge pull request #1738 from RosettaCommons/everyday847/legacy_recces Restore legacy RECCES function

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Merge pull request #1736 from RosettaCommons/jkleman/fix_mploadtime fixing mploadtime integration test for valgrind

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Merge pull request #1733 from RosettaCommons/roccomoretti/clang_SA_fixes2 Some Clang Static Analysis Fixes This hits most of them. The ones that are left are primarily "Value ... is never read" errors. Spot checking these, many (most?) look to be non-trivial. That is, the fact that the variable assignment is not read is pointing to a possible logic error in the code. These will likely need attention from subject-matter experts: src/apps/public/darc/DARC.cc:125 Value stored to 'origin_space' during its initialization is never read src/apps/public/pepspec/pepspec.cc:678 Value stored to 'ref_pep_end' is never read src/apps/public/pepspec/pepspec.cc:680 Value stored to 'this_pep_end' is never read src/apps/public/pepspec/pepspec.cc:745 Value stored to 'ref_pep_end' is never read src/apps/public/pepspec/pepspec.cc:747 Value stored to 'this_pep_end' is never read src/apps/public/pepspec/pepspec_anchor_dock.cc:359 Value stored to 'ref_pep_end' is never read src/apps/public/pepspec/pepspec_anchor_dock.cc:361 Value stored to 'pep_end' is never read src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc:316 Value stored to 'tx' is never read src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc:317 Value stored to 'ty' is never read src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc:318 Value stored to 'tz' is never read src/apps/public/weight_optimization/torsional_potential_corrections.cc:1098 Value stored to 'dist2' is never read src/apps/public/weight_optimization/torsional_potential_corrections.cc:1099 Value stored to 'dist2' is never read src/core/conformation/symmetry/SymmetryInfo.cc:701 Value stored to 'fail' is never read src/core/fragment/util.cc:598 Dereference of null pointer (loaded from variable 'left') src/core/io/silent/RNA_SilentStruct.cc:344 Value stored to 'success' is never read src/core/optimization/Minimizer.cc:517 Value stored to 'FAF' is never read src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc:150 Value stored to 'tried' is never read src/core/scoring/ScoreFunction.cc:2311 Called C++ object pointer is null src/core/scoring/ScoreFunction.cc:2318 Called C++ object pointer is null src/core/scoring/constraints/BigBinConstraint.cc:189 Value stored to 'omega_lower_' is never read src/core/scoring/constraints/BigBinConstraint.cc:190 Value stored to 'omega_upper_' is never read src/core/scoring/constraints/ConstraintIO.cc:358 Value stored to 'start' is never read src/core/scoring/dna/base_geometry.cc:677 Value stored to 'base_flipped' is never read src/core/scoring/dna/base_geometry.cc:1122 Value stored to 'base_flipped' is never read src/core/scoring/dssp/StrandPairing.cc:847 Value stored to 'reg' during its initialization is never read src/core/scoring/facts/FACTSPotential.cc:726 Value stored to 'g2' is never read src/core/scoring/hbonds/hbonds.cc:969 Value stored to 'frac2' is never read src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:466 Value stored to 'layer' is never read src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:468 Value stored to 'layer' is never read src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:549 Value stored to 'layer' is never read src/core/scoring/membrane/FaMPEnvSmoothEnergy.cc:551 Value stored to 'layer' is never read src/core/scoring/membrane/MPEnvEnergy.cc:232 Value stored to 'layer' is never read src/core/scoring/membrane/MPEnvEnergy.cc:234 Value stored to 'layer' is never read src/core/scoring/membrane/MPEnvEnergy.cc:271 Value stored to 'layer' is never read src/core/scoring/membrane/MPEnvEnergy.cc:272 Value stored to 'layer' is never read src/core/scoring/methods/GaussianOverlapEnergy.cc:126 Value stored to 'score' is never read src/core/scoring/methods/GaussianOverlapEnergy.cc:128 Value stored to 'score' is never read src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:444 Value stored to 'layer' is never read src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:446 Value stored to 'layer' is never read src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:522 Value stored to 'layer' is never read src/core/scoring/methods/MembraneEnvSmoothEnergy.cc:524 Value stored to 'layer' is never read src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.cc:316 Value stored to 'l' is never read src/core/scoring/orbitals/OrbitalsScore.cc:418 Value stored to 'orb_orb_E' is never read src/core/scoring/packing/PoseBalls.cc:295 Value stored to 'atype' is never read src/core/scoring/packing/PoseBalls.cc:296 Value stored to 'atype' is never read src/core/scoring/packing/PoseBalls.cc:297 Value stored to 'atype' is never read src/core/scoring/packing/PoseBalls.cc:298 Value stored to 'atype' is never read src/core/scoring/power_diagram/PowerDiagram.cc:1530 Value stored to 'arc_num_m1' is never read src/core/scoring/power_diagram/PowerDiagram.cc:1532 Value stored to 'arc_num_p1' is never read src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc:1578 Value stored to 'atmn' is never read src/devel/denovo_protein_design/DesignRelaxMover.cc:114 Value stored to 'CurrentEnergy' during its initialization is never read src/devel/splice/Splice.cc:657 Value stored to 'nearest_to_from' is never read src/devel/splice/Splice.cc:658 Value stored to 'nearest_to_to' is never read src/devel/splice/Splice.cc:1314 Value stored to 'tail_size' is never read src/devel/splice/Splice.cc:1324 Value stored to 'tail_size' is never read src/protocols/antibody/AntibodyInfo.cc:941 Value stored to 'is_H3' is never read src/protocols/antibody/AntibodyInfo.cc:2114 Value stored to 'k' is never read src/protocols/antibody/ModelCDRH3.cc:238 Value stored to 'unaligned_cdr_loop_end' is never read src/protocols/cartesian/md.cc:1443 Value stored to 'start_score' is never read src/protocols/comparative_modeling/LoopRelaxMover.cc:557 Value stored to 'current_sc' during its initialization is never read src/protocols/comparative_modeling/LoopRelaxMover.cc:736 Value stored to 'current_sc' is never read src/protocols/cryst/refinable_lattice.cc:355 Value stored to 'score' during its initialization is never read src/protocols/denovo_design/components/SheetDB.cc:915 Value stored to 'prev_res' during its initialization is never read src/protocols/enzdes/EnzdesFlexBBProtocol.cc:1865 Value stored to 'frag_unique' is never read src/protocols/enzdes/SecondaryMatchProtocol.cc:683 Value stored to 'all_residues_compatible' is never read src/protocols/enzdes/enzdes_util.cc:688 Value stored to 'found' is never read src/protocols/farna/ErraserMinimizerMover.cc:734 Value stored to 'new_score' is never read src/protocols/floppy_tail/FloppyTailMover.cc:561 Value stored to 'starttime' is never read src/protocols/forge/remodel/RemodelAccumulator.cc:255 Value stored to 'boolReturn' is never read src/protocols/frag_picker/scores/PhiPsiRmsd.cc:180 Value stored to 'stmp' is never read src/protocols/frags/TorsionFragment.cc:836 Value stored to 'pose_nres' during its initialization is never read src/protocols/hybridization/FragmentBiasAssigner.cc:623 Value stored to 'CCsum2' is never read src/protocols/hybridization/TMalign.cc:505 Value stored to 'rms1' is never read src/protocols/hybridization/TMalign.cc:1922 Value stored to 'seq_id' is never read src/protocols/hybridization/TMalign.cc:2119 Value stored to 'TMmax' is never read src/protocols/hybridization/TMalign.cc:2146 Value stored to 'TM' is never read src/protocols/hybridization/TMalign.cc:2177 Value stored to 'simplify_step' is never read src/protocols/hybridization/TMalign.cc:2178 Value stored to 'score_sum_method' is never read src/protocols/loophash/LoopHashLibrary.cc:725 Value stored to 'stop_res' is never read src/protocols/loophash/LoopHashLibrary.cc:726 Value stored to 'start_res' is never read src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc:192 Value stored to 'local_debug' during its initialization is never read src/protocols/loops/loops_main.cc:1399 Value stored to 'cutpoint' is never read src/protocols/make_rot_lib/MakeRotLib.cc:206 Value stored to 'previous_ener' during its initialization is never read src/protocols/make_rot_lib/MakeRotLibMover.cc:499 Value stored to 'previous_ener' during its initialization is never read src/protocols/match/Matcher.cc:922 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:928 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:934 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:940 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:955 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:961 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:967 Value stored to 'failed_cast' is never read src/protocols/match/Matcher.cc:973 Value stored to 'failed_cast' is never read src/protocols/membrane/OptimizeMembranePositionMover.cc:269 Value stored to 'score_new' during its initialization is never read src/protocols/membrane/OptimizeMembranePositionMover.cc:299 Value stored to 'score_old' is never read src/protocols/membrane/OptimizeMembranePositionMover.cc:336 Value stored to 'score_new' during its initialization is never read src/protocols/metal_interface/FindClosestAtom.cc:33 Value stored to 'temp_dis' during its initialization is never read src/protocols/moves/MoverStatus.cc:33 Value stored to 'ms' is never read src/protocols/mpi_refinement/Clusterer.cc:92 Value stored to 'dumm' is never read src/protocols/mpi_refinement/Clusterer.cc:102 Value stored to 'dumm' is never read src/protocols/mpi_refinement/MPI_Refinement.cc:380 Value stored to 'dumm' is never read src/protocols/mpi_refinement/MultiObjective.cc:254 Value stored to 'dumm' is never read src/protocols/mpi_refinement/MultiObjective.cc:260 Value stored to 'dumm' is never read src/protocols/mpi_refinement/MultiObjective.cc:609 Value stored to 'dumm' is never read src/protocols/mpi_refinement/MultiObjective.cc:615 Value stored to 'dumm' is never read src/protocols/mpi_refinement/util.cc:619 Value stored to 'iatm_work' during its initialization is never read src/protocols/noesy_assign/PeakFileFormat.cc:599 Value stored to 'weight' is never read src/protocols/optimize_weights/IterativeOptEDriver.cc:4145 Value stored to 'no_tag_yet_assigned' is never read src/protocols/pockets/Fingerprint.cc:106 Value stored to 'atom_serial_number' during its initialization is never read src/protocols/pockets/Fingerprint.cc:113 Value stored to 'residue_sequence_number' during its initialization is never read src/protocols/pockets/Fingerprint.cc:2136 Value stored to 'Differentiable_score' is never read src/protocols/pockets/Fingerprint.cc:2158 Value stored to 'curr_angle1' during its initialization is never read src/protocols/pockets/Fingerprint.cc:2159 Value stored to 'curr_angle2' during its initialization is never read src/protocols/pockets/Fingerprint.cc:2160 Value stored to 'curr_angle3' during its initialization is never read src/protocols/pockets/PocketGrid.cc:2217 Value stored to 'st' is never read src/protocols/pockets/PocketGrid.cc:2225 Value stored to 'en' is never read src/protocols/pockets/PocketGrid.cc:2241 Value stored to 'st' is never read src/protocols/pockets/PocketGrid.cc:2249 Value stored to 'en' is never read src/protocols/pockets/PocketGrid.cc:2265 Value stored to 'st' is never read src/protocols/pockets/PocketGrid.cc:2273 Value stored to 'en' is never read src/protocols/pockets/PocketGrid.cc:2667 Value stored to 'offset' is never read src/protocols/pockets/PocketGrid.cc:2773 Value stored to 'offset' is never read src/protocols/scoring/ImplicitFastClashCheck.cc:271 Value stored to 'bclash' is never read src/protocols/seeded_abinitio/CoordinateCst.cc:262 Value stored to 'anchor_res' is never read src/protocols/sewing/sampling/MonteCarloAssemblyMover.cc:117 Value stored to 'random_action' during its initialization is never read src/protocols/simple_filters/ResidueIEFilter.cc:321 Value stored to 'whole_pose' during its initialization is never read src/protocols/simple_filters/ResidueIEFilter.cc:322 Value stored to 'whole_interface' during its initialization is never read src/protocols/simple_filters/SheetFilter.cc:1393 Value stored to 'stopp' is never read src/protocols/simple_moves/AddCavitiesMover.cc:155 Value stored to 'Ncb' is never read src/protocols/simple_moves/TailsScoreMover.cc:198 Value stored to 'updated_tail_score' during its initialization is never read src/protocols/sparta/Sparta.cc:761 Value stored to 'pred_shift' is never read src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc:1777 Value stored to 'range_end' is never read src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc:1536 The right operand of '!=' is a garbage value src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc:148 Value stored to 'jump_at_moving_suite' is never read src/protocols/stepwise/modeler/util.cc:386 Value stored to 'found_root' is never read src/protocols/toolbox/DecoySetEvaluation.cc:380 Value stored to 'invn' during its initialization is never read src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc:131 Value stored to 'num_neighbors_' is never read src/protocols/topology_broker/CoordConstraintClaimer.cc:123 Value stored to 'new_root' during its initialization is never read src/protocols/topology_broker/TopologyBroker.cc:826 Value stored to 'ok' is never read src/protocols/viewer/triangleIterator.cc:147 Value stored to 'starting' is never read

• Summary

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