commit c4b8093a8eba55323d2123211222490e29975f74 Date: Sat Oct 29 13:57:42 2016 -0700 Adding a site.settings file for the digs and the hyak cluster so we don't all have to write a user.settings file like chumps. commit 5d86df9ef7476f9e28f587770a73d2d265a7abd1 Date: Fri Oct 28 15:25:17 2016 -0700 Fixing a bug with helical symmetry in make_symmdef file. commit d2d8e4f18962824632aa714132e36f5503caaa6d Merge: 431f6bf 734c555 Date: Fri Oct 28 10:54:55 2016 -0400 Merge pull request #1086 from RosettaCommons/JWLabonte/enzymatic_movers EnzymaticMovers: GlycosyltransferaseMover example This merge introduces a framework for a new concept in Rosetta for `EnzymaticMover`s, `Mover`s that simulate enzymatic reactions of post-translational modifications to `Pose`s, which I introduced at Winter RosettaCON2016. (If interested, view my presentation, which should be available from the Rosetta Commons wiki, or contact me. In short, and `EnzymaticMover` moves "`ResidueType` space" in a `Pose` instead of torsion space and creates starting structures for modeling rather than ending decoys from modeling.) This is a work-in-progress. In its current stage, it only uses sequence information, but it will be expanded to include structural information for the determination of which sites on a `Pose` will be modified. Currently, I have only added a generic, human, glycosyltransferase as an example, which modifies NXS/T sites. This merge includes unit and integration tests. It also, as an aside, includes a sorting of the init files for `Mover`s as a bonus. (Please keep those files clean!) All tests pass. commit 431f6bfe43894647916bfb421bc85b8ee756502e Merge: 8d83a82 37f012e Date: Fri Oct 28 09:35:53 2016 -0400 Merge pull request #1745 from RosettaCommons/dougrenfrew/reorder_mpiworkpartitionjd_jobs Changing the way the WorkPartitionJD splits up jobs commit 8d83a829a8dfaff54e699ef509a021d717673e94 Merge: 52729bb 7eeaba1 Date: Thu Oct 27 18:41:45 2016 -0700 Merge pull request #1739 from RosettaCommons/sboyken/extend_networks Allow HBNet to keep and/or extend existing networks in the input pose if desired commit 52729bbf710231c957c466d349b636b69a6989e7 Date: Thu Oct 27 20:12:13 2016 -0400 Dummy commit to trigger server run commit 00e0410c08ce7b45303aa505b2c731aa4c94083b Date: Thu Oct 27 10:05:49 2016 -0500 Add missing Dumbrack-binary-generating exclusion to the integration test ignore list. commit 8408ec878a834e3f548b07537a7d453788d64d87 Merge: 40555ce c075059 Date: Thu Oct 27 08:39:02 2016 -0400 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!) commit 40555ceaf54e839672fa6cb24278908f90127639 Merge: a358e31 328574c Date: Wed Oct 26 21:52:03 2016 -0600 Merge pull request #1746 Adding sorting to list_dir implementation to improve Rosetta result stability commit a358e31e2d0bb03af9b084198b047354dba9a2a8 Merge: b0520df f9f3fbe Date: Wed Oct 26 17:42:03 2016 -0500 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. commit b0520df3d4c9c14ab8e0548d0c2daa58f0a5f380 Merge: 344661f 94f9172 Date: Wed Oct 26 15:17:31 2016 -0400 Merge pull request #1744 from RosettaCommons/dougrenfrew/optE_override Adding additional overrides to OptE code when compiling with MPI commit 344661fce99d4d823d3fe86facc82e221f8a0db8 Merge: 3a2cb8a 50190a8 Date: Wed Oct 26 11:46:16 2016 -0500 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. commit 3a2cb8a298cfa30908e1c1d6f579da9615c84f28 Date: Tue Oct 25 20:11:44 2016 -0700 Cartoon mode fix changing normalize(15) to normalize(), otherwise the width of cartoon sheets/helices is messed up! commit e5559736dede5cd1349c03305cf496db89756420 Merge: d223e5f b049db9 Date: Tue Oct 25 09:14:53 2016 -0700 Merge pull request #1741 from RosettaCommons/xingjiepan/improve_refactoredKIC_performance Xingjiepan/improve refactored kic performance commit d223e5ff2afa269debdac9bddb14d275acc7e8b6 Merge: 8ceeee8 20f521d Date: Mon Oct 24 21:35:30 2016 -0600 Merge pull request #1740 Updating profile test script so it now check if ‘command’ file is present in test dir. commit 8ceeee875d5a8beb36713d359aa9b483298f190f Merge: 1744519 302dad1 Date: Mon Oct 24 15:02:06 2016 -0500 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. commit 174451937457cb2190c794801cd68bd2904fdb2f Merge: caf3ac9 15f6ade Date: Mon Oct 24 14:59:56 2016 -0500 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. commit caf3ac9d7450e125941c5e85236b57d398680305 Merge: d86bb01 73eb829 Date: Sat Oct 22 12:28:39 2016 -0700 Merge pull request #1156 from RosettaCommons/sboyken/hbnet2master Merge HBNet into master commit d86bb012bfabcde46f43d02b2ec518c1ceb05421 Merge: 1045032 fdfacfb Date: Fri Oct 21 19:56:24 2016 -0700 Merge pull request #1738 from RosettaCommons/everyday847/legacy_recces Restore legacy RECCES function commit 10450323228d4643cd3594f8752d412c33d62d1c Merge: 729dab5 39c8ce3 Date: Fri Oct 21 09:43:39 2016 -0400 Merge pull request #1736 from RosettaCommons/jkleman/fix_mploadtime fixing mploadtime integration test for valgrind commit 729dab5add03eafa7db7371e3817d7a67d853f33 Merge: de5f564 6846a64 Date: Thu Oct 20 10:02:23 2016 -0500 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 commit de5f5645e7092a5d1d64a51fb809a2cd0b987e5b Merge: 0c3dc27 4834fba Date: Wed Oct 19 23:47:33 2016 -0700 Merge pull request #1732 from RosettaCommons/vmullig/vmullig/support_nmethyl_3 Incremental merge #2 of N-methyl support This one fixes a number of bugs and adds support for randomly drawing mainchain torsions biased by the probability distribution from a custom RamaPrePro map. commit 0c3dc27b1bc25aebf9ac631db8150d6719e41eee Merge: 960d3f3 ba4aee4 Date: Wed Oct 19 22:04:04 2016 -0400 Merge pull request #1735 from RosettaCommons/JWLabonte/PyRosetta PyRosetta: Restoring pose_from_pdb() Its absence is wrecking a whole bunch of user's scripts and it is what is published in the Workshops. We can't just go changing the names of functions in PyRosetta so rapidly, so I am restoring the wrapper I added in version 3 that was commented out in version 4. commit 960d3f38963bdf5b95e863e467d0b6e96a73ead0 Merge: bbcf1cd 188016b Date: Wed Oct 19 00:12:34 2016 -0700 Merge pull request #1729 from RosettaCommons/hssnzdh2/cycpep_changes Enabling the use of some ncAAs in simple_cycpep_prediction. This pull request is making small changes (literally adding 4 lines) to simple_cycpep_prediction app and genkic_perturber to use canonical aa rama tables for ncAAs for which a backbone_aa is specified in the params file. This will allow us to forward fold our designed peptides with some common ncAAs. Done: - add the option to SimpleCycpepPredictionApplication - add the option to GeneralizedKICPerturber - set for testing @gbhardwaj @vmullig commit bbcf1cd8480eed63ece05839b30c6eb908f322b6 Merge: fd6de9a e8c0feb Date: Tue Oct 18 18:56:41 2016 -0700 Merge pull request #1724 from RosettaCommons/rhiju/rb_recces Rigid-body RECCES for K_d estimation all tests change a little bit due to residue_types increasing; i have carefully looked at other changes, and they are in the tests that routinely change a tiny bit due to floating point instabilities. commit fd6de9a856a211637c4002c625fefc5b2845d90f Merge: 790b5a8 b8c2e24 Date: Tue Oct 18 15:44:08 2016 -0500 Merge pull request #1731 from RosettaCommons/roccomoretti/sanitizer_unicode_issue Fix sanitizer unicode issue Change the benchmark tests to be more robust to Unicode values in the various output files. commit 790b5a8c10f84d0c14837bb33b2931a5deb53411 Merge: 2722dc0 02872e3 Date: Tue Oct 18 08:29:12 2016 -0700 merge in change from biox3 commit 2722dc066c81bebde3339d87b636348c60b9d992 Date: Tue Oct 18 08:26:16 2016 -0700 fixing compile of pilot app commit 9a13725b606cbe2ec5a2e901aed94219dd1db23d Merge: 5d31834 32f095f Date: Mon Oct 17 13:41:35 2016 -0400 Merge pull request #1713 from RosettaCommons/revert-1712-vmullig/revert_cart_breakages Revert "Reverting pull request 1699 due to breakages of simple_cycpep_predict tests." All issues have been fixed, merging the features back in. commit 5d318346de8d269d57ba2c14f91c2ef2b037053b Date: Sun Oct 16 21:59:49 2016 -0700 Fix the site.settings.qb3 file commit ee9fe0742863c2164a45d5a6782414564faa9771 Merge: 4237fba ed6ae91 Date: Sun Oct 16 16:21:59 2016 -0700 Merge pull request #1723 from RosettaCommons/xingjiepan/fix_LoopModeler_bugs Xingjiepan/fix loop modeler problems commit 4237fba19107da20acfbaf5bc0e2400e7e4b0683 Date: Fri Oct 14 13:32:31 2016 -0400 Carbohydrates/PyRosetta: quick one line bug fix in PyRosetta test commit e8c94d50f446185532819bdc92adc620676618d4 Merge: d6fa73d f1e3532 Date: Thu Oct 13 18:23:23 2016 -0700 Merge pull request #1722 from RosettaCommons/vmullig/cycpep_analysis Adding a pilot app to do some simple analysis on the bin distribution from peptide backbone enumeration. No integration test changes expected. commit d6fa73d98650291726bb7efb6b7c73beadbdf24b Merge: 87ac61c 31b467b Date: Thu Oct 13 20:05:52 2016 -0500 Merge pull request #1721 from RosettaCommons/roccomoretti/using_mac_fix Fix header_using_check integration test grep on Mac apparently formats its output slightly differently than grep on Linux, resulting in issues with the way I set up the header_using_check integration test. commit 87ac61c2ce7da19e5f3d66df965263d5360faafc Merge: 42ec9c6 8e2b04a Date: Thu Oct 13 09:55:26 2016 -0700 Merge pull request #1714 from RosettaCommons/danpf/lapl_master Danpf/lapl master commit 42ec9c6d1d152d7ebd49bea0e1a8c5ebf08bb04e Merge: b029e90 140d979 Date: Wed Oct 12 17:44:24 2016 -0700 Merge pull request #1695 from RosettaCommons/vmullig/eccentricity2 Add a parameter to the Crick parameters to allow lateral sqash of bundles or beta-barrels The old pull request branch was branched off of master with the toxic commit. I've re-pulled (removing the toxic commit), created a new branch, and cherry-picked all of my changes from the old. Tasks: - Add the parameter to functions in numeric. - Add arclength correction factor (t->t' s.t. int(0->t')(|f'(x,epsilon)|dx) = int(0->t)(|f'(x,epsilon=1)|dx)) This is very hard to compute, but as it turns out, the correction factor is negligibly small. - Add correction factor in numeric to normalize the path tangent vector. - Update protocols/helical_bundle/util.cc/hh. - Update MakeBundleHelix mover. - Update PerturbBundleHelix mover. - Update MakeBundle mover. - Update PerturbBundle mover. - Update BundleGridSampler mover. - Update BundleGridSamplerHelper class. - Update BundleParameters class. - Update BundleParametersSet class. Nothing to update. - Update PerturbBundleOptions class. Nothing to update. - Update test_makebundle_mover pilot app. - Integration test. - Documentation. - Beauty. (Note: at some point, I'll properly set things up so that the parametric movers don't need to be updated whenever a new parameter is added to the generating equations. When I initially implemented this, I failed to anticipate the need for this.) commit b029e907a26bbcdb362cfe6c55b6aa72e5c23c8a Date: Wed Oct 12 15:19:40 2016 -0700 Updating site.settings.qb3 * Now pulls environment. Assumes you are using scl enable, e.g. : nohup nice scl enable python27 devtoolset-4 'python scons.py -j16 bin mode=release' & * Removes WError flag * Removes Intel/core2/any other optimization, so that binaries work on AMD nodes commit 5088594daae6abcde385f8ec9dfaedf36eed003c Merge: a826831 3c1cb01 Date: Wed Oct 12 14:53:38 2016 -0700 Merge pull request #1719 from RosettaCommons/vmullig/reinstante_mainchainscoretable Reinstate the merge of the MainchainScoreTable class I think I solved the gcc/release issue. A call to ceil and a cast from float to int were occasionally resulting in the wrong bin being chosen (e.g. 180.0 -math-> 18.0 -ceil-> 19.0 -static_cast-> 19 instead of 18); I don't know why this created an issue only with gcc and only in release mode. But in the context, round made more sense than ceil, and this resolves the scoring issue and preserves old scoring behaviour. commit a8268315d1067c72f53b5d33753f1e6cae011942 Merge: ae611f9 18d5ff1 Date: Wed Oct 12 14:51:19 2016 -0700 Merge pull request #1709 from RosettaCommons/tlinsky/generic_simulated_annealer_to_protcools Move GenericSimulatedAnnealer mover to protocols commit ae611f909b26d5c552b6ef47199b225bdc17e745 Merge: 55631ab ef7ad4b Date: Wed Oct 12 11:28:58 2016 -0500 Merge pull request #1707 from RosettaCommons/roccomoretti/no_using Dis-ab-using Rosetta headers Our coding conventions state that we shouldn't use `using namespace` in the top level of header files. There's a good reason for this: `using namespace` in a header file doesn't just affect that header file, it also affects all subsequent header files and cc files. (Even if the two headers don't directly include each other, but are instead mutually included in a third file, the using declaration from one can change how the other header is parsed.) I'd even go one further: a non-namespace `using` directive in headers is also a bad idea, unless you're explicitly attempting to hoist a symbol from one namespace to the other. (So no using declarations just because you don't want to type "core::" in front of everything.) This pull request removes all `using namespace` from the headers in src, as well as all the convenience `usings` (usings which looked to me to be namespace hoistings were left.) A new integration tests was added, which should fail upon the introduction of a `using namespace` or `using` in the top level of headers. (There's an ignore mechanism for the hoisting usings.) `using`s and `using namepace`s are still permitted in *.cc file, as well as within classes and functions within header files (as the effect is scope limited). I also did not touch the apps/pilot/ or devel/ directories, and the integration test ignores those. commit 55631ab66d815de9288c4cbb09c40d93647cb66f Merge: aa45b56 a3830c0 Date: Wed Oct 12 08:55:05 2016 -0700 Merge pull request #1717 from RosettaCommons/tlinsky/bridgechains_iterations Add option to control #trials in BridgeChainsMover commit aa45b568983e9ede5eb94a573738561e25c99ae1 Merge: 455d70a 1d9ef47 Date: Wed Oct 12 08:54:09 2016 -0700 Merge pull request #1711 from RosettaCommons/tlinsky/disulfidize_silent Disulfidize now adds a pose comment noting where disulfide were created commit 455d70a6d6422335ae4ef02e27594ec8eae80938 Merge: 1b63b0a b0a64dc Date: Wed Oct 12 08:53:45 2016 -0700 Merge pull request #1710 from RosettaCommons/tlinsky/polyxxx_res_selector Add residue selector to MakePolyXMover commit 1b63b0ad23e16fd83fbcd8f1b7387058481a89fb Merge: 5ffae20 354f307 Date: Tue Oct 11 21:56:12 2016 -0700 Merge pull request #1716 from RosettaCommons/vmullig/split_ppi Split the ppi_v3 integration tests to prevent test server failure The ppi_v3 integration test has been failing to complete for months, which trains developers to ignore integration test failure-to-run errors. I'm splitting this test up into several tests, each of which runs in a reasonable amount of time. (To clarify: ppi_v3 applies a few movers, than tests a large number of reporter filters, some of which take a while to calculate what they measure. I'm splitting this into ppi_v3_suiteA, ppi_v3_suiteB, etc., and ensuring that each suite applies all of the movers and a subset of the filters, so that all of the filters are tested, albeit in several small integration tests instead of a single large one.) commit 5ffae202a8b12067a539f192f677cc515288b8cf Merge: 3d4a750 878410d Date: Tue Oct 11 21:53:02 2016 -0700 Merge pull request #1718 from RosettaCommons/vmullig/temporarily_revert_mainchainscoretable Temporarily reverting merge of MainchainScoreTable class while we debug gcc release build Reverting merge of MainchainScoreTable class temporarily while I figure out what the gcc issue is. Details: It seems that there's a gcc-specific scoring bug that crept in, possibly with this merge. It does NOT alter scoring in debug mode or in any clang release compilation. Only the gcc 4.8 release-mode compilation is affected, and it results in RamaPrePro returning NaN for most poses. It's some sort of weird compiler optimization thing that we haven't yet tracked down, but in the interests of keeping master functional, I'll do the detective work in a branch. commit 3d4a750b3d3c8e7a5e2d5cbcc7197b7e34d8371b Merge: 42db744 e380814 Date: Tue Oct 11 11:53:05 2016 -0400 Merge pull request #1715 from RosettaCommons/JWLabonte/sugars/PyRosetta_scripts Carbohydrates/PyRosetta: fix to PyRosetta demo/test for carbohyrdates If this doesn't work, we'll try something else.... commit 42db744670f8a21e3c2972307bb980e5836a5b0e Merge: e747805 5d9a7e7 Date: Mon Oct 10 20:36:40 2016 -0700 Merge pull request #1701 from RosettaCommons/tlinsky/tomponents_multi_bulge Add BuildDeNovoBackbone mover support for multiple bulges per strand The cyclic peptide integration tests failed upon testing, but should be fixed now that Vikram has reverted a commit that broke them. commit e747805349759f67c22fa1ae72750950215a82b5 Merge: 87d6068 64752a9 Date: Mon Oct 10 14:36:00 2016 -0700 Merge pull request #1712 from RosettaCommons/vmullig/revert_cart_breakages Reverting pull request 1699 due to breakages of simple_cycpep_predict tests. @BrandonFrenz: Fix these test breakages in your branch, test on the test server, and then re-merge with master. And the community as a whole needs to start paying more attention to the test server. We had green lights across the board for some time, but now we're starting to ignore breakages. It is NOT a developer's responsibility to keep re-fixing his or her features that someone else has broken, IF those features are covered with tests. It is the rest of the community's responsibility to make sure that they don't break tests. commit 87d6068463afe8c89762f03898f7c34e6405b212 Merge: 2f1118e 605d797 Date: Mon Oct 10 13:36:54 2016 -0400 Merge pull request #1635 from RosettaCommons/JWLabonte/sugars/scoring Carbohydrates: Updating sugar_bb term to score additional linkage types This merge introduces two new CHI Energy Functions (from http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00834) to the `sugar_bb` scoring term for the scoring of exocyclic ψ angles. It also adds two simple parabolic functions to the `sugar_bb` term for the scoring of exocyclic ωs, depending on whether the gauche effect is in play or not. These changes should improve the scoring of sugars. This merge also refactors some lengthy code to remove code duplication, adds some C++11 simplifications, and has fixed several silent bugs. A whole bunch of integration and unit tests were added. carbohydrates, vancomycin, and simple_glycosylation integration test changes are expected. commit 2f1118e7e26c37fe08f6d40540a0dd454ca95b8a Date: Sun Oct 9 11:47:10 2016 -0700 Making sure DockingProtocol gives fullatom output when the user requests it. (only really matters when the user is in low_res_protocol_only mode) commit ca682e793297624b6a3c4b25e9337e441bb03241 Date: Fri Oct 7 20:38:37 2016 -0700 Use unique_ptr commit f8c96207db02b4d23ec02a9977c07ddad711d2ae Merge: e519ba5 f19a188 Date: Fri Oct 7 18:33:19 2016 -0700 Merge pull request #1706 from RosettaCommons/dimaio/fixcrystrefine Bugfix for extra=python build following c++11 changes. commit e519ba5e5965415c155ddca044407f3dd847c989 Merge: 5186ccb db86d85 Date: Fri Oct 7 18:23:56 2016 -0400 Merge pull request #1699 from RosettaCommons/bfrenz/symmetric_edges Bfrenz/symmetric edges commit 5186ccb6c915c804fed24a9c83bb7bd31588e3a2 Merge: c567442 1489a99 Date: Fri Oct 7 13:40:09 2016 -0700 Merge pull request #1694 from RosettaCommons/rhiju/rb_entropy Rhiju/rb entropy Tests pass. Accompanying pull request for demos (also in branch called `rhiju/rb_entropy`) coming soon. commit c5674424e28bc4f354d1f957d1b5f851f2b2d939 Merge: bc19aa9 358e18e Date: Fri Oct 7 09:45:39 2016 -0700 Merge pull request #1698 from RosettaCommons/tlinsky/tomponents Update NamedSegment residue selector commit bc19aa933d2f61f94546dbc797815ca2a51f673f Merge: cfa82e1 08e02b6 Date: Fri Oct 7 09:20:39 2016 -0400 Merge pull request #1678 from RosettaCommons/aleaverfay/sfxn_from_option_collection Initialize ScoreFunction and its derivatives from a local OptionCollection In particular, the EnergyMethodOptions class previously read from the global option system in its constructor. Now, when you call get_score_function with a local OptionCollection object (as people will do in JD3), the OptionCollection is passed along through the ScoreFunction to the EnergyMethodOptions object, and the EnergyMethodOptions object reads from this OptionCollection. This PR brings in two unit tests that ensure that no options read during ScoreFunction initialization from the local option collection are undocumented. The main documentation function is the static method EnergyMethodOptions::list_read_options. commit cfa82e14dd206a72bb9e3b7dd5202bd40e71f08a Merge: 1db1d9f 7a7e1f6 Date: Fri Oct 7 01:03:41 2016 -0700 Merge pull request #1690 from RosettaCommons/everyday847/dont_make_bad_promises You will see all those EnergyMethod integration test changes, just in the other direction. Do not be alarmed. commit 1db1d9f59c7974ee08717af9e593d3a1139cd86c Merge: e28fde1 0fad052 Date: Thu Oct 6 16:27:20 2016 -0600 Merge pull request #1693 from RosettaCommons/sergey/binder PyRosetta update: commit e28fde10bb3d74267512cc5c66b898a47f68e9dc Merge: e827985 4ce3b4c Date: Thu Oct 6 17:13:20 2016 -0500 Merge pull request #1686 from RosettaCommons/roccomoretti/transform_randomizations Transform mover randomization tweaks The Transform mover in ligand docking has a pre-randomization step, but previously you were able to adjust the translational distance in this randomization, but not the magnitude of the rotational randomization. This adds an option which allows you to specify a maximal rotational magnitude (0-360 degrees, defaults to a full 360 randomization.). Also, the translational randomization was slightly skewed, sampling only one octant from the original position. I've changed the sampling method such that the random translation is uniformly in a sphere of the given maximal radius around the starting position. Integration test changes expected from XML-based ligand docking protocols, as this changes the random number pulls involved in setting up the ligand randomization. @darwinyfu Feel free to resolve the merge conflicts with your branch how you like. commit e82798527588b3f5626d2d63625aa904701aae74 Date: Thu Oct 6 13:10:05 2016 -0500 Fix erraser_minimize. Also includes updates to ignore_list to fix code_duplication changes on line addition/removal. commit 0aebded7375d588e4e1df5a5fda0cec7035ebbee Date: Thu Oct 6 13:06:43 2016 -0500 Update ignore_list so that the code_duplication doesn't trigger every code add/remove. commit c80d4b9fb7aa5a872cc48cfd24bd664cad584a3b Merge: a7b2356 b5734ad Date: Thu Oct 6 08:38:27 2016 -0700 Merge pull request #1685 from RosettaCommons/rhiju/thermal_minimizer_tests Rhiju/thermal minimizer tests All tests pass (except floating-point sensitive ones & erraser_minimizer which I think will no longer trigger diffs). commit a7b2356b5151c376a4479e7a8c6710ff57e1ff70 Merge: 3a101b5 9065ff4 Date: Thu Oct 6 00:54:40 2016 -0700 Merge pull request #1696 from RosettaCommons/vmullig/refix_peptidecyclizemover Reinstating Parisa's fix to the PeptideCyclizeMover. One integration test change expected. commit 3a101b52197a4c154903a2d7d899162dc733d121 Date: Wed Oct 5 16:22:04 2016 -0700 Commented out the ifdefs that prevented devel from being used in the Rosetta@home application. Many design filters are in devel that should be useful on Rosetta@home. commit 5033fa2eb31af7788b8c1df94f68584963d1b6bf Date: Wed Oct 5 12:13:57 2016 -0400 Resetting master to 7693ff1 and adding .beaut to the .gitignore file Do not merge your branch into master if it contains the poison commit 99b81fc02, which appeared last night (10/4/2016) at 7pm EDT. How can you know if your branch contains this commit? Run this command in your branch: > git merge-base 99b81fc02 HEAD If it returns 99b81fc02, then it does. How will you fix your branch if you've already merged this commit into it? *sigh* You'll need to create a new branch from the version before you merged master into your branch, and then you'll need to re-merge master and then cherry-pick all subsequent commits you've made to your branch since. BUT you can't do that until after you've cleaned up your version of master. How will you clean up your version of master. One of two ways. > git checkout master; git reset --hard 7693ff1; git pull or > git fetch; git reset origin/master —hard; git branch -d master; git checkout master Hopefully, you did not pull master between last night and this morning, and hopefully you did not merge master into your branch between last night and this morning. But many of you, of course, did. Contact me if you have trouble. aleaverfay@gmail.com. commit 7693ff1bc6d1e99d35e1f3eb0e81eb8d3cf8d963 Merge: 553d4db a03e0d4 Date: Tue Oct 4 08:44:09 2016 -0700 Merge pull request #1682 from RosettaCommons/rhiju/swm_oct3_2016_hotfix Rhiju/swm oct3 2016 hotfix commit 553d4dbab8d1f9ad007624db1efeca8f4d0a16d0 Merge: 50d6eb5 d16b233 Date: Mon Oct 3 14:36:44 2016 -0700 Merge pull request #1683 from RosettaCommons/vmullig/support_nmethyl_merge1 Initial merge of code to support N-methylated peptides I want to split this pull request into a few merges. This one brings in considerably refactored Patch, RamaPrePro, and rotamer code. Lazy loading of any number of mainchain torsion potentials is now supported, and the RamaPrePro score term has been switched over to use the new lazy loading machinery. All integration test changes are expected. #Background and Rationale: N-methyl amino acids can be used during peptide synthesis to confer various desirable properties on a synthetic peptide. N-methylation removes a hydrogen bond donor, in many cases promoting solubility in hydrophobic environments and helping with membrane permeability. It also greatly alters the conformational preferences of an amino acid residue. We want to be able to design with N-methyl amino acids, and this pull request is intended to add support for: - Modelling N-methyl amino acid geometry (adding a patch for N-methylation). - Properly scoring N-methyl amino acid-containing peptides (permitting the loading of custom Ramachandran and p_aa_pp tables for N-methyl amino acids). Following the implementation of PackerPalettes (pull request #1047), a future pull request will add: - Support for designing with N-methyl amino acids (i.e. getting the packer decide whether to N-methylate a position or not). commit 50d6eb5cc4c9ddb35f1b142d673810227184b9df Merge: 7dc0396 c33c606 Date: Mon Oct 3 14:35:06 2016 -0700 Merge pull request #1524 from RosettaCommons/tlinsky/fldsgn-update Fixes to fldsgn classes commit 7dc0396d07ee2aa73174de02bfda3f6b66380245 Merge: 766f395 37a7ee3 Date: Sun Oct 2 20:38:22 2016 -0700 Merge pull request #1660 from RosettaCommons/everyday847/ncnts_in_stepwise NCNTs in stepwise: Integration test changes are all spurious (new EnergyMethodOption, in particular, causes ~50). commit 766f395f217c6411b6d735593c16e93627fa03f0 Merge: 29b1d1a d6f6124 Date: Sun Oct 2 15:03:44 2016 -0700 Merge pull request #1679 from RosettaCommons/everyday847/cache_rna_scoreterms Use extended interface for RNA_FA_Elec commit 29b1d1ae2cc811e97b8ff17a834a688df4af4cd1 Merge: 30ca990 783f124 Date: Sun Oct 2 03:34:30 2016 -0700 Merge pull request #1680 from RosettaCommons/vmullig/brian_sequence_bug Fixing inverted PDBInfo check in Sequence.cc Brian Koepnick and Jeff Flatten of the Foldit team found a bug in Sequence.cc: the existence of a PDBInfo object is checked before the object is accessed, but the check is inverted. That is, the object is accessed ONLY if it doesn't exist, which makes no sense. This fixes that. Thanks to these two for finding this. @bkoepnick @jflat06 commit 30ca990d4d13187accb7fe6ab6b58d6760f704bc Merge: d961d42 8420fee Date: Sat Oct 1 15:25:21 2016 -0700 Merge pull request #1676 from RosettaCommons/tjbrunette/remodel_helical_repeat_test_fix bug fix for remodel_helical_repeat unit test commit d961d42224d8c918539227df36cb128d03f76e1a Merge: 65b9d0d 811506d Date: Fri Sep 30 15:55:30 2016 -0700 Merge pull request #1345 from RosettaCommons/roccomoretti/clang_SA Clang Static Analysis -- is a go! commit 65b9d0de869575abc8c46e46d78057367745d060 Merge: 17b6b26 1408193 Date: Fri Sep 30 15:02:47 2016 -0700 Merge pull request #1663 from RosettaCommons/tlinsky/remove_csts_excn Add option to RemoveConstraints mover whether or not to throw excn commit 17b6b265b230d9268868f6c0d9c6c8c777b099d4 Merge: 7c1e450 f6d4572 Date: Fri Sep 30 12:58:25 2016 -0600 Merge pull request #1677 from RosettaCommons/sergey/binder Adding bindings for operators -= and += commit 7c1e4500c13f3b714c76c570c2de5ef8f51c7ecc Merge: 8a434aa 5289dce Date: Thu Sep 29 20:49:42 2016 -0500 Merge pull request #1675 from RosettaCommons/bazzoli/pwsho-reparam Flags for pwSHO reparameterization commit 8a434aa1028a49288e4cdaf0fb8d1c32c1d528d4 Merge: a893647 130d8d0 Date: Thu Sep 29 15:46:07 2016 -0700 Merge pull request #1671 from RosettaCommons/vmullig/simple_cycpep_predict_features Adding needed features to simple_cycpep_predict application Tasks: - Add options for torsion/angle/length space relaxation with: - Flexible bond angles. - Flexible bond angles and bond lengths. - Add option for full Cartesian-space relaxation. - Have the above options actually trigger appropriate rounds of relaxation. - Bond angles. - Bond angles + bond lengths. - Cartesian-space relaxation. - Integration tests for the above. - Add output of number of cis-peptide bonds. - Plus unit test for sorting by cis-peptide bond count. - Add hard energy cutoff for output. - Add to one integration test. - Turn cis-pro sampling on by default. (Do this last, after confirming that above changes do not change existing behaviour of integration tests.) - Disable cis-pro sampling explicitly in existing integration tests that did not sample cis-pro before. - Documentation. - Beauty. commit a8936474a5a5430bccafdeb8bb6ac2fbeaa9523f Date: Thu Sep 29 15:41:59 2016 -0700 Reverting build breakage commit 55c2d680f0efa25e4ccdd71302a3a47cb3769650 Date: Thu Sep 29 11:55:41 2016 -0700 added option to thermal_sampler to sample varying bb angles, compiles successfully commit e71b3a8b59bdbc3ede6252e2274eb070bb59f721 Merge: f7fd13f a8acc2c Date: Wed Sep 28 18:22:48 2016 -0700 Merge pull request #1670 from RosettaCommons/jadolfbr/ab_h3_valgrind Jadolfbr/ab h3 valgrind Fix antibody_H3 valgrind issue for camelid antibodies. Note that the valgrind test was done here: http://benchmark.graylab.jhu.edu/revision?id=4809&branch= Integration tests are cosmetic commit f7fd13f5ed4c94114539c2382ef636e1405c2804 Date: Wed Sep 28 16:56:08 2016 -0500 Fixing Rosetta build on Stampede commit a589a9d03c59faea0d4dfcd001daa425f009529e Merge: 1b549ce 3eb4373 Date: Wed Sep 28 14:56:21 2016 -0700 Merge pull request #1669 from RosettaCommons/vmullig/simple_cycpep_predict_features_firstmerge Splitting pull request for simple_cycpep_predict Since there will be some integration test changes, I want to merge this first part before the second part. Tasks: - Add options for torsion/angle/length space relaxation with: - Flexible bond angles. - Flexible bond angles and bond lengths. - Add option for full Cartesian-space relaxation. - Have the above options actually trigger appropriate rounds of relaxation. - Bond angles. - Bond angles + bond lengths. - Cartesian-space relaxation. - Integration tests for the above. - Documentation. - Beauty. commit 1b549ceb53c1dccfcf79050a00d31166a980dc2a Merge: 1229251 9a19ae5 Date: Wed Sep 28 10:06:40 2016 -0700 Merge pull request #1659 from RosettaCommons/tjbrunette/repeat_fusion Tjbrunette/repeat fusion adds code for repeat fusion, code for calculating energy using Will's motifs, and a way to very accurately fix short loops ideally, and code that was necessary to propagate hemes. Will try to do smaller merges from here on out. commit 1229251b8d131c94b2636a3aff0c368efe6b9781 Date: Wed Sep 28 09:49:54 2016 -0500 Fix erraser_minimize integration tests on Macs. GNU and MacOS sed are stupidly incompatible. commit ebecc749a8b3955c80b575096c316d7d96a3b76c Merge: 6b6ba53 b0f91ef Date: Tue Sep 27 22:07:08 2016 -0700 Merge pull request #1639 from RosettaCommons/everyday847/thermal_sampler_mover The ThermalSamplingMover now exists for all your thermal sampling needs, as does the ThermalMinimizer as a stepwise plug-in. commit 6b6ba53c43da53895ea698b88f196b1bf1807733 Merge: ba3cec3 90840af Date: Tue Sep 27 18:04:45 2016 -0700 Merge pull request #1666 from RosettaCommons/vmullig/add_betapatch_test Adding beta_patch scoring test. The -beta_patch flag is currently completely untested. I WILL break this without a test. commit ba3cec3c6444e077c375a0194bfce42d5aac2a77 Merge: f279414 0f9fe7a Date: Tue Sep 27 12:53:01 2016 -0700 Merge pull request #1665 from RosettaCommons/hahnbeom/beta_patch_fix simple fix to FastDesign + beta_patch commit f279414251c3e9759f756fa5e9af3ce03c4d3570 Merge: db1cc22 7b0382b Date: Tue Sep 27 14:37:42 2016 -0500 Merge pull request #1657 from RosettaCommons/roccomoretti/san_benchmark Hook sanitizers into the benchmark testing system. I was slightly mistaken in the earlier sanitizer pull request, in that setting up unit/integration tests for different "mode" builds are more complicated. This pull request sets things up so the test system can run the sanitizer unit/integration tests. (They currently fail, but they run.) Also, we've been rather overzealous in the integration test ignore settings. e.g. we excluded "time", which will also exclude lines containing "runtime error" or other such ("antimetabolite", for example). I tweaked the ignore exceptions to be more specific, as a consequence massive integration test changes are expected, as lines which were ignored will be ignored no longer. If there is some tracer line which I revealed which should probably be hidden, feel free to add a specific line to the ignore_list: just be as specific with the regex as possible, to avoid inadvertent hiding of lines. commit db1cc228bdae771380c2fa3379b2be70b723a4c6 Merge: ce96515 dcdf0f0 Date: Tue Sep 27 14:01:48 2016 -0500 Merge pull request #1658 from RosettaCommons/roccomoretti/atompaircst_pdbnumber_fix Fix PDB number parsing in Constraints Around July of this year a change was made to the constraint parsing code, such that how PDB numbering for chain A in constraint files was altered. This bug has been fixed, and a new unit test which should catch a similar error has been added. With some changes in the demos repository that have already been made, this should fix all of the tutorials tests, allowing us to enable those for routine running. commit ce96515174faf4a2d4bd806914fbf6ee5f2528e0 Merge: 2783bfc 6e3ae46 Date: Tue Sep 27 08:37:40 2016 -0400 Merge pull request #1662 from RosettaCommons/lqtza/make-antibody-relax-consistent FastRelax() in antibody.cc now respects coordinate constraints. commit 2783bfca2d94f79e44f55d6a5e85b80b94b69f04 Merge: 0323c75 f49d544 Date: Tue Sep 27 11:19:08 2016 +0300 Merge pull request #1647 from RosettaCommons/orlypolo/add-FPD-metrices Orlypolo/add fpd metrices commit 0323c759152a0722246f16a434012831ad27c69d Merge: 7ff5adc 9acfd6a Date: Mon Sep 26 13:39:09 2016 -0700 Merge pull request #1661 from RosettaCommons/vmullig/kinclose_symm Adding unit tests for symmetric bridgeObjects behaviour (underlying all kinematic closure). I need to make sure that mirror-image systems yield mirror-image solutions. Which they do. Good. commit 7ff5adc73cd05a785e162ef89491768ffdd4de13 Merge: 18a0b45 f351b39 Date: Mon Sep 26 15:55:30 2016 -0400 Merge pull request #1337 from RosettaCommons/aleaverfay/jd3_jobdist_jobqueen_interface Fleshed out interface between JD3's JD and JQ when the JQ is interested in describing multiple-round protocols. The JQ describes the interdependencies between batches of jobs using a directed graph; each node represents a batch of jobs (all of which are independent of each other) and a directed edge from i to j implies that the jobs for node j will not be started until after the jobs from node i have completed. commit 18a0b457963d971ac5f02cdfef0d9a0e8ff28e8b Merge: e3b6a47 ac0bddc Date: Mon Sep 26 13:40:22 2016 +0200 Merge pull request #1642 from RosettaCommons/jaumebonet/psipred_input Psipred parser function overload. commit e3b6a47df729cfc79889e0fee2f0fc8f6adc8b83 Merge: 2a7a11f a528e66 Date: Sat Sep 24 21:50:19 2016 -0600 Merge pull request #1655 from RosettaCommons/sergey/mi PyRosetta: Adding support for multiple inheritance, adding bindings for operator* and operator/, adding PyMOL-Rosetta server script. commit 2a7a11fccdbbbfd767fb1951370078b71befa3c4 Merge: af7a7aa 7f6bf35 Date: Fri Sep 23 10:10:02 2016 -0700 Merge pull request #1656 from RosettaCommons/tjbrunette/place_motifs_master Tjbrunette/place motifs master adds the code for Jorge/Will's place motifs mover to master. commit af7a7aa6e1dc2a7d5d256ef96f939ea6b153ae88 Merge: 218ff1c 6f0f9f3 Date: Fri Sep 23 10:01:21 2016 -0500 Merge pull request #1503 from RosettaCommons/roccomoretti/rts_type Separate the concept of a ResidueTypeSet "type" from a RTS "name" There is (or should be) a distinction between the "type" of a ResidueTypeSet (e.g. "Fullatom"/"Centoid") and the "name" of the ResidueTypeSet. For example, we have an fa_standard RT, but doesn't that imply there could be an fa_nonstandard? This pull request attempts to separate out the concept of a TypeSet type (as an enum), and replace the instances of using names as comparisons with types (where it makes sense). This means that you can now ask "is this residue a 'fullatom' residue type, rather than asking "is this ResidueType a member of the fa_standard ResidueTypeSet. A bunch of integration test changes expected, as I made SwitchResidueTypeSet much less chatty when it's "switching" a pose that already has residues of the desired type. commit 218ff1c5abbd71057cd228ccd62b62c8bf18a754 Merge: 31b773b fa4649e Date: Fri Sep 23 09:44:41 2016 -0500 Merge pull request #1654 from RosettaCommons/roccomoretti/fix_gcc47_segfault Fix GCC segfault issue. Older versions (4.7.2, 4.8.1) of GCC have internal compiler errors (the compiler segfaults) with code in SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh. Separating out the variable initialization over two lines 'fixes' the issue and allows Rosetta to be compiled. commit 31b773b3312e277bf795c0ceaa61ec568fcaf22d Merge: ff6a10c d6b5eab Date: Thu Sep 22 15:00:21 2016 -0700 Merge pull request #1649 from RosettaCommons/hahnbeom/cartbonded_redefine redefining names of subterms in cart_bonded: commit ff6a10c31e0e78db1d5a88a5550ab24464e5b664 Merge: c652a28 d98b292 Date: Thu Sep 22 13:19:59 2016 -0700 Merge pull request #1652 from RosettaCommons/vmullig/chunli_metal_issue Fixing crash with -auto_setup_metals when poses were resized Correcting issue that lead to crashes whenever -auto_setup_metals was used with a pose that was subsequently resized. Since NamedAtomPairConstraint and NamedAngleConstraint didn't implement a remap_resid() function, the parent class (AtomPairConstraint or AngleConstraint) function was called, resulting in the NamedAtomPairConstraint being replaced with an AtomPairConstraint, or the NamedAngleConstraint being replaced with an AngleConstraint, with atom IDs set to zero. commit c652a282cb5ddac31f0d415eb2e59a598cc8b25f Merge: 100af89 2f405ed Date: Thu Sep 22 10:42:48 2016 -0400 Beautifying two files commit 100af89f5bd8d6b2c75094dcfd331d4e1a5cae7d Date: Thu Sep 22 10:42:30 2016 -0400 Beautifying two files commit 419a6e6112f4565097bde2908f4154117f828985 Merge: 036ab7d 503ff60 Date: Wed Sep 21 11:31:08 2016 -0700 Merge pull request #1591 from RosettaCommons/everyday847/chemical_mapping_utils DMS potential refactor: Use MathNTensor in place of nested vector commit 036ab7df2218820f8d14df42d6b408eb4f0e0636 Date: Tue Sep 20 16:43:07 2016 -0700 Adding the appropriate version number mapping for macOS sierra (also el capitan - I dropped the ball on that one) commit 25448b44ebbbfb0c3e48753c70feaf06d45c1f20 Merge: dbc6e36 87a07e4 Date: Tue Sep 20 17:03:13 2016 -0500 Merge pull request #1643 from RosettaCommons/roccomoretti/fix_option_space_parsing Fix option space parsing regression A feature used relatively frequently by the Meiler Lab in ligand docking is the ability to concatenate PDBs by quoting. e.g. -s "protein.pdb ligand.pdb" instead of manually concatenating the two PDBs into a single-file complex. A recent change to the option system broke this functionality. (It would also break other situations where you'd have a space in a file name.) Surprisingly, the functionality appears not to have been tested. This commit restores the previous behavior, as well as adding tests to confirm the functionality is preserved. commit dbc6e36b1ecddab1f40ba71f93df8a9ffeeab7d7 Merge: ec6c9ef ebb5e52 Date: Tue Sep 20 14:47:55 2016 -0700 Merge pull request #1623 from RosettaCommons/hssnzdh2/close_bond close bond commit ec6c9efda055aaf20d6be30a1252e9157075e473 Merge: 16b0001 93469d7 Date: Tue Sep 20 14:29:35 2016 -0700 Merge pull request #1640 from RosettaCommons/vmullig/cyclic_cart2 Splitting cyclic Cartesian pull request so that I can merge in the stuff that IS working now. I'm still having trouble with symmetric glycine minimization, for reasons to be determined. This pull request will merge in fixes to the following: - Using cart_bonded with cyclic geometry. - Using cart_bonded with D-amino acids. - Unit test coverage for cart_bonded with cyclic geometry and D-amino acids. Tests of symmetric glycine minimization are temporarily commented out. commit 16b000136d88f1a9e8d8847ae7dd11fd6adfd628 Merge: 871701a da8c2aa Date: Tue Sep 20 11:04:54 2016 -0500 Merge pull request #1633 from RosettaCommons/roccomoretti/sanitize Add compiler "sanitizer" error-checking builds to Rosetta Recent versions of Clang and GCC have "sanitizer" options which will compile with extra instrumentation to catch various dodgy dealings. I've added Scons modes (not extras) for three of the santizers. * mode=addsan The AddresSanitizer which detects memory errors, such as trying to access memory you're not supposed to. This includes the LeakSanitizer, which catches memory leaks. * mode=ubsan The UndefinedBehaviorSanitizer catches instances where you're doing certain things in the code which are "undefined behavior" according to the C++11 standard. * mode=memsan The MemorySanitizer attempts to detect uninitialized reads. (Like Valgrind.) -- This is not (yet?) supported under GCC, and is only of minimal use with Clang, as you also need to have a special compilation of the C++ standard library. I include it for the intrepid. Testing for addsan/memsan/ubsan errors is easy - simply run unit or integration tests with the build for the appropriate "mode" (using a recent compiler which supports them). If an error is encountered, a message will be printed to stdout, and the test will "crash" in a way that's recognizable to the testing system. (The leak detection of addsan, which prints but does not cause an error-code exit.) Debugging of ubsan errors is easier if you first set the UBSAN_OPTIONS=print_stacktrace=1 environment variable prior to running the tests. This pull request also contains some "low hanging fruit" fixes for errors in addsan and ubsan builds. continuous_sewing_hasher and discontinuous_sewing_hasher integration test changes expected, as they were over-writing log files commit 871701a9f8de5b803bb7058f1ba90fb260924387 Merge: 39f23e9 bb1682e Date: Tue Sep 20 10:58:29 2016 -0400 Merge pull request #1638 from RosettaCommons/Cyrus/mergetarget From Steven Lewis: 99% of this is a refactor of the coupled_moves application into a protocol-scale Mover (so it has both a protocol Mover and a small-scale Mover), so that the whole protocol can be called by other code. This will be of interest to @kylebarlow and @nollikai . There are expected integration test changes to the coupled_moves test, as its tracer changes from apps to protocols. If you account for that (cat ref/coupled_moves/log_* | sed 's/^apps.c//' > tmp1; cat new/coupled_moves/log_* | sed 's/^protocols.c//' > tmp2; diff tmp1 tmp2 you will see that the only change is the addition of a "don*e" marker at the end of the application. 1% of this is a trivial typo fix in ExtendChainMover, which will probably disinterest @tlinsky . commit 39f23e91120f4e62e0c1c2ddbcfc33ec81c43ac0 Merge: 602e5d3 6e17a2f Date: Tue Sep 20 00:16:59 2016 -0400 Merge pull request #1589 from RosettaCommons/mlnance/site_constraints_use_carbohydrate_C1 Refactored SiteConstraint to allow for carbohydrate chains commit 602e5d37b1f0febf2bdee5ed34ba232353813cac Merge: db3198f 173eca5 Date: Sat Sep 17 10:58:59 2016 -0400 Merge pull request #1617 from RosettaCommons/lqtza/prepack-enhancements-with-modernization Lqtza/prepack enhancements with modernization commit db3198f5b0b00b4588de0e5c8e2c2ef83d16f603 Merge: 7e1a46e a951f19 Date: Sat Sep 17 10:57:11 2016 -0400 Merge pull request #1578 from RosettaCommons/lqtza/com_ft Enable center-of-mass fold tree in FT commit 7e1a46e958885d5b2244267f0bbd66f75ade5a1e Merge: f434624 dd65384 Date: Sat Sep 17 00:38:30 2016 -0400 Merge pull request #1607 from RosettaCommons/JWLabonte/sugars/modified_sugars Carbohydrates: Improving IUPAC sequence input for non-standard/modified sugar cases carbohydrate integration test changes expected. commit f434624d377f3a890c0cc273e11d362a21a3eb3b Merge: 563a2ea bdee303 Date: Fri Sep 16 16:48:21 2016 -0700 Merge pull request #1532 from RosettaCommons/daslab/thermal_sampler Daslab/thermal sampler commit 563a2ea09dcf1404108a30e7de5a91d6ed561ebf Merge: a208a45 f549121 Date: Fri Sep 16 08:17:47 2016 -0400 Merge pull request #1625 from RosettaCommons/lqtza/fix-antibody-orientation-alignment Lqtza/fix antibody orientation alignment commit a208a451c4eb284d989930fef349d300691f208b Date: Thu Sep 15 19:20:12 2016 -0700 I'm clearly too tired. Merged the wrong way. Reverting. commit 27a5f65d4ee88ca7af3e20b4160589c564ecbee0 Merge: 63da017 6161c19 Date: Thu Sep 15 19:18:48 2016 -0700 Merging master into vmullig/cyclic_cart. commit 63da01749a47ebe27a99f7b42b833b65b50d94d8 Date: Thu Sep 15 15:39:14 2016 -0700 Updating user.settings.template with os.environ line. commit 3d74bc6794b70162872d6406ca35b19875a78716 Merge: 3114825 e8ed38c Date: Thu Sep 15 14:35:36 2016 -0700 Merge pull request #1626 from RosettaCommons/vmullig/modvartypeselector Switch the ModifyVariantTypeMover to use ResidueSelectors instead of TaskOperations Tasks: - Remove TaskOperation code. - Add setters and getters for ResidueSelector. - Add ResidueSelector XML parsing. - Modify apply() function. - Fix segfault. - Turns out that CTERM_AMIDATION has not been added to the VariantTypes list. - It also turns out that the patch file has a number of other problems. Fixed now. - Integration test. - Documentation. - Beauty.